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pysam-developers / pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
https://pysam.readthedocs.io/en/latest/
MIT License
782 stars 274 forks source link

Cannot install pysam #682

Closed krat19 closed 6 years ago

krat19 commented 6 years ago

Hello, I have been trying to install pysam but get the following lengthy error message. Could anyone please help?

$ pip install pysam Collecting pysam Using cached https://files.pythonhosted.org/packages/fc/9b/4bb8d016406dcff47e2866e14d3dcb10741ec3920649e8c521996830944f/pysam-0.14.1.tar.gz Installing collected packages: pysam Running setup.py install for pysam ... error Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-record-ni9iS8/install-record.txt --single-version-externally-managed --compile:

pysam: no cython available - using pre-compiled C

# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Darwin... Darwin dylib
checking how to run the C preprocessor... gcc -E
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... no
checking for lzma_easy_buffer_encode in -llzma... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... yes
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: config.h is unchanged
# pysam: htslib configure options: --enable-libcurl
make: ./version.sh: Command not found
make: ./version.sh: Command not found
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lcurl
# pysam: htslib_config PLATFORM=Darwin
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
# pysam: htslib_config LDFLAGS=
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: HAVE_COMMONCRYPTO=1
# pysam: config_option: HAVE_GMTIME_R=1
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_IRODS=0
# pysam: config_option: HAVE_LIBCURL=1
# pysam: config_option: HAVE_MMAP=1
running install
running build
running build_py
creating build
creating build/lib.macosx-10.13-intel-2.7
creating build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/__init__.py -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/bcftools.py -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/config.py -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/Pileup.py -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/samtools.py -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/utils.py -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/version.py -> build/lib.macosx-10.13-intel-2.7/pysam
creating build/lib.macosx-10.13-intel-2.7/pysam/include
copying pysam/include/__init__.py -> build/lib.macosx-10.13-intel-2.7/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
package init file 'htslib/__init__.py' not found (or not a regular file)
package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
copying pysam/libcalignedsegment.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libcbcf.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libcbcftools.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libcfaidx.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libchtslib.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libcsamfile.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libcsamtools.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libctabix.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libctabixproxies.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libcutils.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/libcvcf.pxd -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/cbcftools_util.h -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/csamtools_util.h -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/htslib_util.h -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/pysam_stream.h -> build/lib.macosx-10.13-intel-2.7/pysam
copying pysam/pysam_util.h -> build/lib.macosx-10.13-intel-2.7/pysam
creating build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/bam.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/bam2bcf.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/bam_endian.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/bedidx.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/config.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/sam.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/sam_header.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/sample.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/samtools.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/samtools.pysam.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/tmp_file.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
copying samtools/version.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools
creating build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/bam2bcf.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/bin.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/call.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/config.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/convert.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/gvcf.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/kheap.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/ploidy.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/regidx.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/vcfbuf.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
copying bcftools/version.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/bcftools
creating build/lib.macosx-10.13-intel-2.7/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/samtools/win32
creating build/lib.macosx-10.13-intel-2.7/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib
copying htslib/config.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib
copying htslib/hfile_internal.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib
copying htslib/hts_internal.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib
copying htslib/textutils_internal.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib
copying htslib/thread_pool_internal.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib
copying htslib/version.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib
creating build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_os.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.macosx-10.13-intel-2.7/pysam/include/htslib/htslib
running build_ext
building 'pysam.libchtslib' extension
creating build/temp.macosx-10.13-intel-2.7
creating build/temp.macosx-10.13-intel-2.7/pysam
creating build/temp.macosx-10.13-intel-2.7/htslib
creating build/temp.macosx-10.13-intel-2.7/htslib/cram
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/libchtslib.c -o build/temp.macosx-10.13-intel-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from pysam/libchtslib.c:438:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from pysam/libchtslib.c:439:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam/htslib_util.h:4:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
2 warnings generated.
In file included from pysam/libchtslib.c:439:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam/htslib_util.h:4:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
pysam/libchtslib.c:5240:17: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'Py_ssize_t' (aka 'long') [-Wshorten-64-to-32]
  __pyx_v_off = hseek(__pyx_v_self->fp, __pyx_v_offset, __pyx_v_whence);
              ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/htslib_util.c -o build/temp.macosx-10.13-intel-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from pysam/htslib_util.c:5:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from pysam/htslib_util.c:9:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam/htslib_util.h:5:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf.h:40:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
pysam/htslib_util.c:36:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
      b->m_data = size;
                ~ ^~~~
pysam/htslib_util.c:53:22: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
  int d = nbytes_new - nbytes_old;
      ~   ~~~~~~~~~~~^~~~~~~~~~~~
4 warnings generated.
In file included from pysam/htslib_util.c:5:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/kfunc.c -o build/temp.macosx-10.13-intel-2.7/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/knetfile.c -o build/temp.macosx-10.13-intel-2.7/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
htslib/knetfile.c:234:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        return strtol(ftp->response, &p, 0);
        ~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/knetfile.c:240:15: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    int len = strlen(cmd);
        ~~~   ^~~~~~~~~~~
htslib/knetfile.c:305:13: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        l = p - fn - 6;
          ~ ~~~~~~~^~~
htslib/knetfile.c:381:13: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        l = p - fn - 7;
          ~ ~~~~~~~^~~
htslib/knetfile.c:432:8: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        ret = strtol(buf + 8, &p, 0); // HTTP return code
            ~ ^~~~~~~~~~~~~~~~~~~~~~
5 warnings generated.
htslib/knetfile.c:193:47: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wshorten-64-to-32]
                curr = netread(fd, (void*)((char*)buf + l), rest);
                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/knetfile.h:35:45: note: expanded from macro 'netread'
#define netread(fd, ptr, len) read(fd, ptr, len)
                              ~~~~          ^~~
htslib/knetfile.c:545:9: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'ssize_t' (aka 'long') [-Wshorten-64-to-32]
        return l;
        ~~~~~~ ^
2 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/kstring.c -o build/temp.macosx-10.13-intel-2.7/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/kstring.c:34:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
htslib/kstring.c:98:16: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        int p = buf+20-cp;
            ~   ~~~~~~^~~
htslib/kstring.c:135:11: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        int sl = strlen(cp);
            ~~   ^~~~~~~~~~
htslib/kstring.c:209:6: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        l = strlen(s);
          ~ ^~~~~~~~~
htslib/kstring.c:258:34: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                if (fgets_fn(s->s + s->l, s->m - s->l, fp) == NULL) break;
                    ~~~~~~~~              ~~~~~^~~~~~
htslib/kstring.c:342:29: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep);
                      ~~~~~~~      ^~~~~~~~~~~
htslib/kstring.c:342:47: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep);
                      ~~~~~~~                        ^~~~~~~~~~~
htslib/kstring.c:347:37: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return (char*)kmemmem(str, n, pat, strlen(pat), _prep);
                      ~~~~~~~              ^~~~~~~~~~~
8 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/bcf_sr_sort.c -o build/temp.macosx-10.13-intel-2.7/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/bcf_sr_sort.c:27:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/bcf_sr_sort.h:37:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/synced_bcf_reader.h:59:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/bcf_sr_sort.c:27:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/bcf_sr_sort.h:37:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/synced_bcf_reader.h:60:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf.h:40:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
htslib/bcf_sr_sort.c:57:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int i, n = bs1->n;
           ~   ~~~~~^
htslib/bcf_sr_sort.c:119:16: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    int alen = strlen(avar->str);
        ~~~~   ^~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:120:16: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    int blen = strlen(bvar->str);
        ~~~~   ^~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:230:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(int, iv->nvar, iv->mvar, iv->var);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:250:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand(bcf1_t*,buf->nrec,buf->mrec,buf->rec);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:313:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(char*,srt->noff,srt->mcharp,srt->charp);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:323:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        int len = strlen(srt->charp[i]);
            ~~~   ^~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:332:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(int,idx+1,srt->mactive,srt->active);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:339:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(int,idx+1,srt->mactive,srt->active);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:382:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand(int,reader->nbuffer,srt->moff,srt->off);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:391:46: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            srt->off[srt->noff++] = srt->str.l;
                                  ~ ~~~~~~~~~^
htslib/bcf_sr_sort.c:409:54: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            int ret, var_idx = 0, var_end = srt->str.l;
                                  ~~~~~~~   ~~~~~~~~~^
htslib/bcf_sr_sort.c:426:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                hts_expand0(var_t,srt->nvar,srt->mvar,srt->var);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:440:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            hts_expand0(int*, var->nvcf, var->mvcf, var->vcf);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:446:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            hts_expand(var_t,grp.nvar,grp.mvar,grp.var);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:454:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            hts_expand0(grp_t, srt->ngrp, srt->mgrp, srt->grp);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:486:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand0(varset_t, srt->nvset, srt->mvset, srt->vset);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:490:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand0(var_t, vset->nvar, vset->mvar, vset->var);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:514:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(int, srt->ngrp*srt->nvset, srt->mpmat, srt->pmat);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bcf_sr_sort.c:515:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(int, srt->nvset, srt->mcnt, srt->cnt);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
22 warnings generated.
In file included from htslib/bcf_sr_sort.c:27:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/bcf_sr_sort.h:37:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/synced_bcf_reader.h:59:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/bgzf.c -o build/temp.macosx-10.13-intel-2.7/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/bgzf.c:38:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
htslib/bgzf.c:372:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
    zs.avail_in = slen;
                ~ ^~~~
htslib/bgzf.c:374:48: warning: implicit conversion loses integer precision: 'unsigned long' to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
    zs.avail_out = *dlen - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
                 ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:393:11: warning: implicit conversion loses integer precision: 'uLong' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    crc = crc32(crc32(0L, NULL, 0L), (Bytef*)src, slen);
        ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:393:51: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
    crc = crc32(crc32(0L, NULL, 0L), (Bytef*)src, slen);
          ~~~~~                                   ^~~~
htslib/bgzf.c:395:42: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    packInt32((uint8_t*)&dst[*dlen - 4], slen);
    ~~~~~~~~~                            ^~~~
htslib/bgzf.c:405:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
    zs->avail_in  = slen;
                  ~ ^~~~
htslib/bgzf.c:407:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
    zs->avail_out = *dlen;
                  ~ ^~~~~
htslib/bgzf.c:438:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    return comp_size;
    ~~~~~~ ^~~~~~~~~
htslib/bgzf.c:447:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
    zs.avail_in = slen;
                ~ ^~~~
htslib/bgzf.c:449:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
    zs.avail_out = *dlen;
                 ~ ^~~~~
htslib/bgzf.c:485:19: warning: implicit conversion loses integer precision: 'uLong' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    uint32_t c1 = crc32(0L, (unsigned char *)fp->uncompressed_block, dlen);
             ~~   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:485:70: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
    uint32_t c1 = crc32(0L, (unsigned char *)fp->uncompressed_block, dlen);
                  ~~~~~                                              ^~~~
htslib/bgzf.c:492:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    return dlen;
    ~~~~~~ ^~~~
htslib/bgzf.c:502:39: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
            fp->gz_stream->avail_in = hread(fp->fp, fp->compressed_block, BGZF_BLOCK_SIZE);
                                    ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:693:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        fp->block_clength = j->comp_len;
                          ~ ~~~^~~~~~~~
htslib/bgzf.c:694:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        fp->block_length = j->uncomp_len;
                         ~ ~~~^~~~~~~~~~
htslib/bgzf.c:731:17: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        count = hread(fp->fp, fp->uncompressed_block, BGZF_MAX_BLOCK_SIZE);
              ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:768:17: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        count = hread(fp->fp, header, sizeof(header));
              ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:788:92: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
            count = hread(fp->fp, cblock+sizeof(header), BGZF_BLOCK_SIZE - sizeof(header)) + sizeof(header);
                  ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
htslib/bgzf.c:850:17: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        count = hread(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
              ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:895:63: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        copy_length = length - bytes_read < available? length - bytes_read : available;
                    ~                                  ~~~~~~~^~~~~~~~~~~~
htslib/bgzf.c:1037:13: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
    count = hpeek(fp->fp, header, sizeof(header));
          ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:1051:13: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
    count = hread(fp->fp, header, sizeof(header));
          ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:1064:13: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
    count = hread(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
          ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:1432:52: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        if (copy_length > remaining) copy_length = remaining;
                                                 ~ ^~~~~~~~~
htslib/bgzf.c:1457:39: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
        int copy_length = ublock_size - fp->block_offset;
            ~~~~~~~~~~~   ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
htslib/bgzf.c:1458:52: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        if (copy_length > remaining) copy_length = remaining;
                                                 ~ ^~~~~~~~~
htslib/bgzf.c:1607:9: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
    n = hread(fp, buf, 16);
      ~ ^~~~~~~~~~~~~~~~~~
htslib/bgzf.c:1675:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    return str->l;
    ~~~~~~ ~~~~~^
htslib/bgzf.c:1816:41: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
    fp->idx->noffs = fp->idx->moffs = x + 1;
                                    ~ ~~^~~
htslib/bgzf.c:1928:36: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
        fp->block_offset = uoffset - fp->idx->offs[i].uaddr;
                         ~ ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
32 warnings generated.
In file included from htslib/bgzf.c:38:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
htslib/bgzf.c:1457:39: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
        int copy_length = ublock_size - fp->block_offset;
            ~~~~~~~~~~~   ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
htslib/bgzf.c:1816:41: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
    fp->idx->noffs = fp->idx->moffs = x + 1;
                                    ~ ~~^~~
htslib/bgzf.c:1928:36: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
        fp->block_offset = uoffset - fp->idx->offs[i].uaddr;
                         ~ ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
htslib/bgzf.c:1937:16: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'long' [-Wshorten-64-to-32]
    return fp->uncompressed_address;    // currently maintained only when reading
    ~~~~~~ ~~~~^~~~~~~~~~~~~~~~~~~~
5 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/errmod.c -o build/temp.macosx-10.13-intel-2.7/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/errmod.c:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
htslib/errmod.c:33:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSORT_INIT_GENERIC(uint16_t)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/ksort.h:293:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
                                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/ksort.h:272:12: note: expanded from macro 'KSORT_INIT'
                for (i = n; i > 1; --i) {                                                                               \
                       ~ ^
2 warnings generated.
In file included from htslib/errmod.c:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/faidx.c -o build/temp.macosx-10.13-intel-2.7/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/faidx.c:42:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from htslib/faidx.c:43:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
htslib/faidx.c:453:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    *len = l < INT_MAX ? l : INT_MAX;
         ~               ^
htslib/faidx.c:561:33: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    return kh_val(fai->hash, k).len;
    ~~~~~~ ~~~~~~~~~~~~~~~~~~~~~^~~
htslib/faidx.c:580:51: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
                                        ~ ~~~~~~~~^~~
htslib/faidx.c:582:51: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    else if(val.len <= p_end_i) p_end_i = val.len - 1;
                                        ~ ~~~~~~~~^~~
6 warnings generated.
In file included from htslib/faidx.c:43:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
htslib/faidx.c:427:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'long' [-Wshorten-64-to-32]
                         + beg % val->line_blen, SEEK_SET);
                         ^~~~~~~~~~~~~~~~~~~~~~
htslib/faidx.c:521:51: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'long' [-Wshorten-64-to-32]
        end = i < k? strtol(s + i, &ep, 10) : val.len;
            ~                                 ~~~~^~~
htslib/faidx.c:532:31: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'long' [-Wshorten-64-to-32]
    } else beg = 0, end = val.len;
                        ~ ~~~~^~~
htslib/faidx.c:533:35: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'long' [-Wshorten-64-to-32]
    if (beg >= val.len) beg = val.len;
                            ~ ~~~~^~~
htslib/faidx.c:534:35: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'long' [-Wshorten-64-to-32]
    if (end >= val.len) end = val.len;
                            ~ ~~~~^~~
htslib/faidx.c:561:33: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    return kh_val(fai->hash, k).len;
    ~~~~~~ ~~~~~~~~~~~~~~~~~~~~~^~~
htslib/faidx.c:580:51: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
                                        ~ ~~~~~~~~^~~
htslib/faidx.c:582:51: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    else if(val.len <= p_end_i) p_end_i = val.len - 1;
                                        ~ ~~~~~~~~^~~
9 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/hfile.c -o build/temp.macosx-10.13-intel-2.7/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/hfile.c:37:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hfile_internal.h:32:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/textutils_internal.h:32:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
htslib/hfile.c:410:19: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        int ret = flush_buffer(fp);
            ~~~   ^~~~~~~~~~~~~~~~
In file included from htslib/hfile.c:735:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
3 warnings generated.
htslib/hfile.c:632:36: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'unsigned long' [-Wshorten-64-to-32]
            char *t = realloc(buf, buf_a);
                      ~~~~~~~      ^~~~~
htslib/hfile.c:637:42: warning: implicit conversion loses integer precision: 'long long' to 'size_t' (aka 'unsigned long') [-Wshorten-64-to-32]
        len = hread(fp, buf+buf_sz, buf_a-buf_sz);
              ~~~~~                 ~~~~~^~~~~~~
htslib/hfile.c:645:56: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wshorten-64-to-32]
    mem_fp = hfile_init_fixed(sizeof(hFILE), "r", buf, buf_sz, buf_a);
             ~~~~~~~~~~~~~~~~                          ^~~~~~
htslib/hfile.c:645:64: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wshorten-64-to-32]
    mem_fp = hfile_init_fixed(sizeof(hFILE), "r", buf, buf_sz, buf_a);
             ~~~~~~~~~~~~~~~~                                  ^~~~~
In file included from htslib/hfile.c:735:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
5 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/hfile_net.c -o build/temp.macosx-10.13-intel-2.7/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/hfile_net.c:30:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hfile_internal.h:32:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/textutils_internal.h:32:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/hts.c -o build/temp.macosx-10.13-intel-2.7/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/hts.c:39:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/hts.c:41:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:77:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/sam_header.h:56:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from htslib/hts.c:41:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/hts.c:141:19: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
    zs.avail_in = npeek;
                ~ ^~~~~
htslib/hts.c:143:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
    zs.avail_out = destsize;
                 ~ ^~~~~~~~
htslib/hts.c:564:20: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        o->val.i = strtol(val, &endp, 0);
                 ~ ^~~~~~~~~~~~~~~~~~~~~
htslib/hts.c:582:55: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        o->opt = CRAM_OPT_REQUIRED_FIELDS, o->val.i = strtol(val, NULL, 0);
                                                    ~ ^~~~~~~~~~~~~~~~~~~~
htslib/hts.c:586:51: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        o->opt = CRAM_OPT_LOSSY_NAMES, o->val.i = strtol(val, NULL, 0);
                                                ~ ^~~~~~~~~~~~~~~~~~~~
htslib/hts.c:594:49: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        o->opt = HTS_OPT_BLOCK_SIZE, o->val.i = strtol(val, NULL, 0);
                                              ~ ^~~~~~~~~~~~~~~~~~~~
htslib/hts.c:679:19: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        len = str - str_start;
            ~ ~~~~^~~~~~~~~~~
htslib/hts.c:1117:34: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        if (ret >= 0) ret = str->l;
                          ~ ~~~~~^
htslib/hts.c:1150:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            hts_expand(char*,n,m,s);
            ^~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts.c:1164:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                hts_expand(char*,n,m,s);
                ^~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts.c:1219:15: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    int len = strlen(fname);
        ~~~   ^~~~~~~~~~~~~
htslib/hts.c:1262:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSORT_INIT(_off, hts_pair64_t, pair64_lt)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/ksort.h:272:12: note: expanded from macro 'KSORT_INIT'
                for (i = n; i > 1; --i) {                                                                               \
                       ~ ^
htslib/hts.c:1263:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSORT_INIT(_off_max, hts_pair64_max_t, pair64_lt)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/ksort.h:272:12: note: expanded from macro 'KSORT_INIT'
                for (i = n; i > 1; --i) {                                                                               \
                       ~ ^
htslib/hts.c:1336:16: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    beg = _beg >> min_shift;
        ~ ~~~~~^~~~~~~~~~~~
htslib/hts.c:1337:22: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    end = (_end - 1) >> min_shift;
        ~ ~~~~~~~~~~~^~~~~~~~~~~~
htslib/hts.c:1347:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
        l->m = new_m;
             ~ ^~~~~
htslib/hts.c:1946:15: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        b = t + (beg>>s); e = t + (end>>s); n = e - b + 1;
          ~ ~~^~~~~~~~~~
htslib/hts.c:1946:33: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        b = t + (beg>>s); e = t + (end>>s); n = e - b + 1;
                            ~ ~~^~~~~~~~~~
htslib/hts.c:1973:15: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        b = t + (beg>>s); e = t + (end>>s);
          ~ ~~^~~~~~~~~~
htslib/hts.c:1973:33: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        b = t + (beg>>s); e = t + (end>>s);
                            ~ ~~^~~~~~~~~~
htslib/hts.c:2481:35: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        while (isdigit_c(*s)) e = push_digit(e, *s++);
                                ~ ^~~~~~~~~~~~~~~~~~~
htslib/hts.c:2511:73: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    *beg = hts_parse_decimal(colon+1, &hyphen, HTS_PARSE_THOUSANDS_SEP) - 1;
         ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
htslib/hts.c:2515:37: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    else if (*hyphen == '-') *end = hts_parse_decimal(hyphen+1, NULL, HTS_PARSE_THOUSANDS_SEP);
                                  ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts.c:2707:45: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                iter->curr_reg = (found_reg - iter->reg_list);
                               ~  ~~~~~~~~~~^~~~~~~~~~~~~~~~
htslib/hts.c:2779:21: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        while ((l = hread(remote_hfp, buf, buf_size)) > 0) {
                  ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts.c:2819:12: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    l_fn = strlen(fn); l_ext = strlen(ext);
         ~ ^~~~~~~~~~
htslib/hts.c:2819:32: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    l_fn = strlen(fn); l_ext = strlen(ext);
                             ~ ^~~~~~~~~~~
htslib/hts.c:2837:12: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    l_fn = strlen(local_fn);
         ~ ^~~~~~~~~~~~~~~~
34 warnings generated.
In file included from htslib/hts.c:39:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/hts.c:41:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/hts.c:1102:16: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'long' [-Wshorten-64-to-32]
        return htell(fp->fp.hfile);
        ~~~~~~ ^~~~~~~~~~~~~~~~~~~
htslib/hts.c:1336:16: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    beg = _beg >> min_shift;
        ~ ~~~~~^~~~~~~~~~~~
htslib/hts.c:1337:22: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    end = (_end - 1) >> min_shift;
        ~ ~~~~~~~~~~~^~~~~~~~~~~~
htslib/hts.c:1946:15: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        b = t + (beg>>s); e = t + (end>>s); n = e - b + 1;
          ~ ~~^~~~~~~~~~
htslib/hts.c:1946:33: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        b = t + (beg>>s); e = t + (end>>s); n = e - b + 1;
                            ~ ~~^~~~~~~~~~
htslib/hts.c:1973:15: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        b = t + (beg>>s); e = t + (end>>s);
          ~ ~~^~~~~~~~~~
htslib/hts.c:1973:33: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        b = t + (beg>>s); e = t + (end>>s);
                            ~ ~~^~~~~~~~~~
htslib/hts.c:2481:35: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        while (isdigit_c(*s)) e = push_digit(e, *s++);
                                ~ ^~~~~~~~~~~~~~~~~~~
htslib/hts.c:2511:73: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    *beg = hts_parse_decimal(colon+1, &hyphen, HTS_PARSE_THOUSANDS_SEP) - 1;
         ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
htslib/hts.c:2515:37: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    else if (*hyphen == '-') *end = hts_parse_decimal(hyphen+1, NULL, HTS_PARSE_THOUSANDS_SEP);
                                  ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
15 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/hts_os.c -o build/temp.macosx-10.13-intel-2.7/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/md5.c -o build/temp.macosx-10.13-intel-2.7/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/md5.c:52:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
In file included from htslib/md5.c:52:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/multipart.c -o build/temp.macosx-10.13-intel-2.7/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/multipart.c:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from htslib/multipart.c:33:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
2 warnings generated.
In file included from htslib/multipart.c:33:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/probaln.c -o build/temp.macosx-10.13-intel-2.7/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/probaln.c:33:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
In file included from htslib/probaln.c:33:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/realn.c -o build/temp.macosx-10.13-intel-2.7/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/realn.c:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
In file included from htslib/realn.c:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/regidx.c -o build/temp.macosx-10.13-intel-2.7/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/regidx.c:28:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/regidx.c:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
htslib/regidx.c:132:37: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    kputsn(chr_from, chr_to-chr_from+1, &idx->str);
    ~~~~~~           ~~~~~~~~~~~~~~~^~
htslib/regidx.c:137:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand0(reglist_t,idx->nseq,idx->mseq,idx->seq);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/regidx.c:138:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand0(char*,idx->nseq,m_prev,idx->seq_names);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/regidx.c:146:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(reg_t,list->nregs,list->mregs,list->regs);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/regidx.c:176:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
            int len = strlen(fname);
                ~~~   ^~~~~~~~~~~~~
htslib/regidx.c:196:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    idx->payload_size = payload_size;
                      ~ ^~~~~~~~~~~~
htslib/regidx.c:302:18: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    reg->start = hts_parse_decimal(ss, &se, 0);
               ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/regidx.c:306:46: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    reg->end = hts_parse_decimal(ss, &se, 0) - 1;
             ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
htslib/regidx.c:327:48: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    reg->start = hts_parse_decimal(ss, &se, 0) - 1;
               ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
htslib/regidx.c:335:20: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        reg->end = hts_parse_decimal(ss, &se, 0);
                 ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12 warnings generated.
In file included from htslib/regidx.c:28:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
htslib/regidx.c:302:18: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    reg->start = hts_parse_decimal(ss, &se, 0);
               ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/regidx.c:306:46: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    reg->end = hts_parse_decimal(ss, &se, 0) - 1;
             ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
htslib/regidx.c:327:48: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    reg->start = hts_parse_decimal(ss, &se, 0) - 1;
               ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
htslib/regidx.c:335:20: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        reg->end = hts_parse_decimal(ss, &se, 0);
                 ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/sam.c -o build/temp.macosx-10.13-intel-2.7/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/sam.c:35:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/sam.c:37:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:77:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/sam_header.h:56:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from htslib/sam.c:37:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/sam.c:136:17: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
    magic_len = bgzf_read(fp, buf, 4);
              ~ ^~~~~~~~~~~~~~~~~~~~~
htslib/sam.c:254:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
        name_len = strlen(p) + 1;
                 ~ ~~~~~~~~~~^~~
htslib/sam.c:287:33: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    return k == kh_end(d)? -1 : kh_val(d, k);
    ~~~~~~                      ^~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/khash.h:516:23: note: expanded from macro 'kh_val'
#define kh_val(h, x) ((h)->vals[x])
                      ^~~~~~~~~~~~
htslib/sam.c:384:33: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    cigar_st = (uint8_t*)cigar0 - b->data;
             ~ ~~~~~~~~~~~~~~~~~^~~~~~~~~
htslib/sam.c:387:26: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    CG_st = CG - b->data - 2;
          ~ ~~~~~~~~~~~~~^~~
htslib/sam.c:440:16: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    if ((ret = bgzf_read(fp, &block_len, 4)) != 4) {
             ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/sam.c:531:47: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cigar_st = (uint8_t*)bam_get_cigar(b) - b->data;
                 ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
htslib/sam.c:713:12: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    return bgzf_seek(fd, offset, whence);
    ~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/sam.c:892:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                    ln = strtol(q + 3, (char**)&q, 10);
                       ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/sam.c:1001:41: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            kputsn(fp->line.s, fp->line.l, &str);
            ~~~~~~             ~~~~~~~~~^
htslib/sam.c:1013:36: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                kputsn(line.s, tab - line.s, &str);
                ~~~~~~         ~~~~^~~~~~~~
htslib/sam.c:1024:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        h = sam_hdr_parse(str.l, str.s);
            ~~~~~~~~~~~~~ ~~~~^
htslib/sam.c:1025:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        h->l_text = str.l; h->text = str.s;
                  ~ ~~~~^
htslib/sam.c:1143:37: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        h->l_text = (beg - h->text) + (h->text + h->l_text - end);
                  ~ ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/sam.c:1198:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    kputsn_(q, p - q, &str);
    ~~~~~~~    ~~^~~
htslib/sam.c:1213:32: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    c->pos = strtol(p, &p, 10) - 1;
           ~ ~~~~~~~~~~~~~~~~~~^~~
htslib/sam.c:1232:22: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        c->n_cigar = n_cigar;
                   ~ ^~~~~~~
htslib/sam.c:1236:41: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
            cigar[i] = strtol(q, &q, 10)<<BAM_CIGAR_SHIFT;
                     ~ ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
htslib/sam.c:1261:33: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    c->mpos = strtol(p, &p, 10) - 1;
            ~ ~~~~~~~~~~~~~~~~~~^~~
htslib/sam.c:1268:16: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    c->isize = strtol(p, &p, 10);
             ~ ^~~~~~~~~~~~~~~~~
htslib/sam.c:1273:27: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
        c->l_qseq = p - q - 1;
                  ~ ~~~~~~^~~
htslib/sam.c:1311:47: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                    kputc_('c', &str); kputc_(x, &str);
                                       ~~~~~~ ^
htslib/sam.c:1318:31: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
                    i32_to_le(x, (uint8_t *) str.s + str.l);
                    ~~~~~~~~~ ^
htslib/sam.c:1324:47: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                    kputc_('C', &str); kputc_(x, &str);
                                       ~~~~~~ ^
htslib/sam.c:1331:31: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                    u32_to_le(x, (uint8_t *) str.s + str.l);
                    ~~~~~~~~~ ^
htslib/sam.c:1346:45: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            kputc_(type, &str);kputsn_(q, p - q, &str); // note that this include the trailing NULL
                               ~~~~~~~    ~~^~~
htslib/sam.c:1381:65: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
            else if (type == 'i') while (q + 1 < p) { i32_to_le(strtol(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
                                                      ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~
htslib/sam.c:1382:65: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
            else if (type == 'I') while (q + 1 < p) { u32_to_le(strtoul(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
                                                      ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~
htslib/sam.c:1390:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    b->data = (uint8_t*)str.s; b->l_data = str.l; b->m_data = str.m;
                                         ~ ~~~~^
htslib/sam.c:1390:67: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    b->data = (uint8_t*)str.s; b->l_data = str.l; b->m_data = str.m;
                                                            ~ ~~~~^
htslib/sam.c:1402:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    b->data = (uint8_t*)str.s; b->l_data = str.l; b->m_data = str.m;
                                         ~ ~~~~^
htslib/sam.c:1402:67: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    b->data = (uint8_t*)str.s; b->l_data = str.l; b->m_data = str.m;
                                                            ~ ~~~~^
htslib/sam.c:1576:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    return str->l;
    ~~~~~~ ~~~~~^
htslib/sam.c:1606:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        return fp->line.l;
        ~~~~~~ ~~~~~~~~~^
htslib/sam.c:1944:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        format_len = opts-format;
                   ~ ~~~~^~~~~~~
htslib/sam.c:1947:22: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        format_len = strlen(format);
                   ~ ^~~~~~~~~~~~~~
htslib/sam.c:1979:28: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    if ( end!=str ) return flag;    // the conversion was successful
                    ~~~~~~ ^~~~
htslib/sam.c:2001:12: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    return flag;
    ~~~~~~ ^~~~
44 warnings generated.
In file included from htslib/sam.c:35:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/sam.c:37:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/sam.c:287:33: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    return k == kh_end(d)? -1 : kh_val(d, k);
    ~~~~~~                      ^~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/khash.h:516:23: note: expanded from macro 'kh_val'
#define kh_val(h, x) ((h)->vals[x])
                      ^~~~~~~~~~~~
htslib/sam.c:713:12: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    return bgzf_seek(fd, offset, whence);
    ~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
7 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.macosx-10.13-intel-2.7/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/synced_bcf_reader.c:34:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/synced_bcf_reader.h:59:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/synced_bcf_reader.c:34:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/synced_bcf_reader.h:60:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf.h:40:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
htslib/synced_bcf_reader.c:133:33: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                kputsn(prev, tmp-prev, &str);
                ~~~~~~       ~~~^~~~~
htslib/synced_bcf_reader.c:807:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand(region1_t,creg->nregs+1,creg->mregs,creg->regs);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:830:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        kputsn(sp,ep-sp,&tmp);
        ~~~~~~    ~~^~~
htslib/synced_bcf_reader.c:834:20: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            from = hts_parse_decimal(sp,(char**)&ep,0);
                 ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:853:18: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            to = hts_parse_decimal(sp,(char**)&ep,0);
               ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:900:23: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        *from = *to = hts_parse_decimal(ss, &tmp, 0);
                    ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:906:21: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            *from = hts_parse_decimal(ss, &tmp, 0);
                  ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:908:19: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            *to = hts_parse_decimal(ss, &tmp, 0);
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:918:19: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            *to = hts_parse_decimal(ss, &tmp, 0);
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:920:21: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            *from = hts_parse_decimal(ss, &tmp, 0);
                  ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:956:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        int len = strlen(regions);
            ~~~   ^~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:1165:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand(char*,reg->nals,reg->mals,reg->als);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:1174:25: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            kputsn(ss,se-ss,&reg->als_str);
            ~~~~~~    ~~^~~
htslib/synced_bcf_reader.c:1175:126: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            if ( &reg->als_str.s[reg->als_str.l] - reg->als[reg->nals] > max_len ) max_len = &reg->als_str.s[reg->als_str.l] - reg->als[reg->nals];
                                                                                           ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:1181:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        kputsn(ss,se-ss,&reg->als_str);
        ~~~~~~    ~~^~~
htslib/synced_bcf_reader.c:1182:122: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        if ( &reg->als_str.s[reg->als_str.l] - reg->als[reg->nals] > max_len ) max_len = &reg->als_str.s[reg->als_str.l] - reg->als[reg->nals];
                                                                                       ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
18 warnings generated.
In file included from htslib/synced_bcf_reader.c:34:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/synced_bcf_reader.h:59:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
htslib/synced_bcf_reader.c:834:20: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            from = hts_parse_decimal(sp,(char**)&ep,0);
                 ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:853:18: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            to = hts_parse_decimal(sp,(char**)&ep,0);
               ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:900:23: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        *from = *to = hts_parse_decimal(ss, &tmp, 0);
                    ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:906:21: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            *from = hts_parse_decimal(ss, &tmp, 0);
                  ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:908:19: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            *to = hts_parse_decimal(ss, &tmp, 0);
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:918:19: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            *to = hts_parse_decimal(ss, &tmp, 0);
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/synced_bcf_reader.c:920:21: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
            *from = hts_parse_decimal(ss, &tmp, 0);
                  ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
8 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.macosx-10.13-intel-2.7/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/vcf_sweep.c:27:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf_sweep.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/vcf_sweep.c:27:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf_sweep.h:30:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf.h:40:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
htslib/vcf_sweep.c:62:36: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    int len = t - rec->d.allele[0] + 1;
        ~~~   ~~~~~~~~~~~~~~~~~~~~~^~~
htslib/vcf_sweep.c:76:36: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    int len = t - rec->d.allele[0] + 1;
        ~~~   ~~~~~~~~~~~~~~~~~~~~~^~~
htslib/vcf_sweep.c:79:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(char, len, sw->mlals, sw->lals);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf_sweep.c:101:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand0(bcf1_t, sw->nrec+1, sw->mrec, sw->rec);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf_sweep.c:167:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            hts_expand(uint64_t, sw->nidx, sw->midx, sw->idx);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
7 warnings generated.
In file included from htslib/vcf_sweep.c:27:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf_sweep.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
htslib/vcf_sweep.c:88:35: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'long' [-Wshorten-64-to-32]
    int ret = hts_useek(sw->file, sw->idx[sw->iidx], 0);
              ~~~~~~~~~           ^~~~~~~~~~~~~~~~~
htslib/vcf_sweep.c:137:29: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'long' [-Wshorten-64-to-32]
        hts_useek(sw->file, sw->idx[0], 0);
        ~~~~~~~~~           ^~~~~~~~~~
3 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/tbx.c -o build/temp.macosx-10.13-intel-2.7/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/tbx.c:33:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/tbx.h:30:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/tbx.c:36:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:31:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/textutils_internal.h:32:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
htslib/tbx.c:75:33: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    return k == kh_end(d)? -1 : kh_val(d, k);
    ~~~~~~                      ^~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/khash.h:516:23: note: expanded from macro 'kh_val'
#define kh_val(h, x) ((h)->vals[x])
                      ^~~~~~~~~~~~
htslib/tbx.c:148:37: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    if (tbx_parse1(&tbx->conf, str->l, str->s, intv) == 0) {
        ~~~~~~~~~~             ~~~~~^
htslib/tbx.c:175:38: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        *tid = intv.tid; *beg = intv.beg; *end = intv.end;
                              ~ ~~~~~^~~
htslib/tbx.c:175:55: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        *tid = intv.tid; *beg = intv.beg; *end = intv.end;
                                               ~ ~~~~~^~~
htslib/tbx.c:203:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        int x = strlen(name[i]) + 1;
            ~   ~~~~~~~~~~~~~~~~^~~
htslib/tbx.c:236:53: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        ret = hts_idx_push(tbx->idx, intv.tid, intv.beg, intv.end, bgzf_tell(fp), 1);
              ~~~~~~~~~~~~                     ~~~~~^~~
htslib/tbx.c:236:63: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        ret = hts_idx_push(tbx->idx, intv.tid, intv.beg, intv.end, bgzf_tell(fp), 1);
              ~~~~~~~~~~~~                               ~~~~~^~~
htslib/tbx.c:356:15: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        tid = kh_val(d,k);
            ~ ^~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/khash.h:516:23: note: expanded from macro 'kh_val'
#define kh_val(h, x) ((h)->vals[x])
                      ^~~~~~~~~~~~
10 warnings generated.
In file included from htslib/tbx.c:33:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/tbx.h:30:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
htslib/tbx.c:75:33: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    return k == kh_end(d)? -1 : kh_val(d, k);
    ~~~~~~                      ^~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/khash.h:516:23: note: expanded from macro 'kh_val'
#define kh_val(h, x) ((h)->vals[x])
                      ^~~~~~~~~~~~
htslib/tbx.c:175:38: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        *tid = intv.tid; *beg = intv.beg; *end = intv.end;
                              ~ ~~~~~^~~
htslib/tbx.c:175:55: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        *tid = intv.tid; *beg = intv.beg; *end = intv.end;
                                               ~ ~~~~~^~~
htslib/tbx.c:236:53: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        ret = hts_idx_push(tbx->idx, intv.tid, intv.beg, intv.end, bgzf_tell(fp), 1);
              ~~~~~~~~~~~~                     ~~~~~^~~
htslib/tbx.c:236:63: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        ret = hts_idx_push(tbx->idx, intv.tid, intv.beg, intv.end, bgzf_tell(fp), 1);
              ~~~~~~~~~~~~                               ~~~~~^~~
htslib/tbx.c:356:15: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        tid = kh_val(d,k);
            ~ ^~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/khash.h:516:23: note: expanded from macro 'kh_val'
#define kh_val(h, x) ((h)->vals[x])
                      ^~~~~~~~~~~~
7 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/textutils.c -o build/temp.macosx-10.13-intel-2.7/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/textutils.c:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from htslib/textutils.c:33:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
htslib/textutils.c:183:33: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                kputsn(buf, lim - buf, d);
                ~~~~~~      ~~~~^~~~~
3 warnings generated.
In file included from htslib/textutils.c:33:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/thread_pool.c -o build/temp.macosx-10.13-intel-2.7/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/vcf.c -o build/temp.macosx-10.13-intel-2.7/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/vcf.c:38:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf.h:39:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/vcf.c:38:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf.h:40:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
htslib/vcf.c:296:14: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    int n = q-p;
        ~   ~^~
htslib/vcf.c:297:41: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    if ( *q!='=' || !n ) { *len = q-line+1; return NULL; } // wrong format
                                ~ ~~~~~~^~
htslib/vcf.c:311:25: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        *len = q - line + (*q ? 1 : 0); // Skip \n but not \0
             ~ ~~~~~~~~~^~~~~~~~~~~~~~
htslib/vcf.c:329:14: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        n = q-p;
          ~ ~^~
htslib/vcf.c:338:29: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            *len = q - line + (*q ? 1 : 0);
                 ~ ~~~~~~~~~^~~~~~~~~~~~~~
htslib/vcf.c:342:38: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        bcf_hrec_add_key(hrec, p, q-p-m);
        ~~~~~~~~~~~~~~~~          ~~~^~
htslib/vcf.c:361:51: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        bcf_hrec_set_val(hrec, hrec->nkeys-1, p, r-p, quoted);
        ~~~~~~~~~~~~~~~~                         ~^~
htslib/vcf.c:374:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    *len = q - line + (*q ? 1 : 0);
         ~ ~~~~~~~~~^~~~~~~~~~~~~~
htslib/vcf.c:391:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    hts_expand0(bcf_idpair_t,hdr->n[dict_type],hdr->m[dict_type],hdr->id[dict_type]);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:430:19: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            idx = strtol(hrec->vals[idx], &tmp, 10);
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:464:19: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            idx = strtol(hrec->vals[i], &tmp, 10);
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:946:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    u32_to_le(htxt.l, hlen);
    ~~~~~~~~~ ~~~~~^
htslib/vcf.c:1232:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(bcf_fmt_t, rec->n_fmt, dec->m_fmt, dec->fmt);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:1253:33: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        dec->fmt[i].p_len = dst - dec->fmt[i].p;
                          ~ ~~~~^~~~~~~~~~~~~~~
htslib/vcf.c:1282:69: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    if ( line->d.id && strcmp(line->d.id, ".") ) bcf_enc_vchar(str, strlen(line->d.id), line->d.id);
                                                 ~~~~~~~~~~~~~      ^~~~~~~~~~~~~~~~~~
htslib/vcf.c:1290:28: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        bcf_enc_vchar(str, strlen(line->d.allele[i]), line->d.allele[i]);
        ~~~~~~~~~~~~~      ^~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:1291:55: warning: implicit conversion loses integer precision: 'unsigned long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    if ( !line->rlen && line->n_allele ) line->rlen = strlen(line->d.allele[0]);
                                                    ~ ^~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:1334:36: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        line->unpack_size[0] = tmp.l; prev_len = tmp.l;
                             ~ ~~~~^
htslib/vcf.c:1337:38: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        line->unpack_size[1] = tmp.l - prev_len; prev_len = tmp.l;
                             ~ ~~~~~~^~~~~~~~~~
htslib/vcf.c:1340:38: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        line->unpack_size[2] = tmp.l - prev_len;
                             ~ ~~~~~~^~~~~~~~~~
htslib/vcf.c:1360:36: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        line->unpack_size[0] = tmp.l; prev_len = tmp.l;
                             ~ ~~~~^
htslib/vcf.c:1368:63: warning: implicit conversion loses integer precision: 'unsigned long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
            if ( !line->rlen && line->n_allele ) line->rlen = strlen(line->d.allele[0]);
                                                            ~ ^~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:1371:38: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        line->unpack_size[1] = tmp.l - prev_len; prev_len = tmp.l;
                             ~ ~~~~~~^~~~~~~~~~
htslib/vcf.c:1383:42: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
            line->unpack_size[2] = tmp.l - prev_len;
                                 ~ ~~~~~~^~~~~~~~~~
htslib/vcf.c:1396:53: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        int size = line->shared.l - (size_t)ptr_ori + (size_t)line->shared.s;
            ~~~~   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:1527:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    x[0] = v->shared.l + 24; // to include six 32-bit integers
         ~ ~~~~~~~~~~~~^~~~
htslib/vcf.c:1528:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    x[1] = v->indiv.l;
         ~ ~~~~~~~~~^
htslib/vcf.c:1569:65: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                kputs("##contig=<ID=", &txt); kputsn(tmp.s, tab - tmp.s, &txt);
                                              ~~~~~~        ~~~~^~~~~~~
htslib/vcf.c:1578:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        kputsn(s->s, s->l, &txt);
        ~~~~~~       ~~~^
htslib/vcf.c:1603:69: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
            bcf_hrec_set_val(hrec, hrec->nkeys-1, (char*) names[i], strlen(names[i]), 0);
            ~~~~~~~~~~~~~~~~                                        ^~~~~~~~~~~~~~~~
htslib/vcf.c:1687:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    if ( len ) *len = txt.l;
                    ~ ~~~~^
htslib/vcf.c:1718:15: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        ret = bgzf_write(fp->fp.bgzf, htxt.s, htxt.l);
            ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:1720:15: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        ret = hwrite(fp->fp.hfile, htxt.s, htxt.l);
            ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:1871:36: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        int l = ((s->l + 7)>>3<<3) - s->l;
            ~   ~~~~~~~~~~~~~~~~~~~^~~~~~
htslib/vcf.c:2009:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        f->offset = mem->l;
                  ~ ~~~~~^
htslib/vcf.c:2042:68: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
                        else x[l++] = (strtol(t, &t, 10) + 1) << 1 | is_phased;
                                    ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
htslib/vcf.c:2060:35: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
                    else x[l++] = strtol(t, &t, 10);
                                ~ ^~~~~~~~~~~~~~~~~
htslib/vcf.c:2210:54: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            if (strcmp(p, ".")) bcf_enc_vchar(str, q - p, p);
                                ~~~~~~~~~~~~~      ~~^~~
htslib/vcf.c:2213:34: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            bcf_enc_vchar(str, q - p, p);
            ~~~~~~~~~~~~~      ~~^~~
htslib/vcf.c:2214:42: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
            v->n_allele = 1, v->rlen = q - p;
                                     ~ ~~^~~
htslib/vcf.c:2219:46: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                        bcf_enc_vchar(str, r - t, t);
                        ~~~~~~~~~~~~~      ~~^~~
htslib/vcf.c:2320:48: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                        bcf_enc_vchar(str, end - val, val);
                        ~~~~~~~~~~~~~      ~~~~^~~~~
htslib/vcf.c:2341:44: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
                                val_a[i] = strtol(t, &te, 10);
                                         ~ ^~~~~~~~~~~~~~~~~~
htslib/vcf.c:2403:23: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    fmt->p_off  = ptr - ptr_start;
                ~ ~~~~^~~~~~~~~~~
htslib/vcf.c:2406:22: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    fmt->p_len = ptr - fmt->p;
               ~ ~~~~^~~~~~~~
htslib/vcf.c:2416:27: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    info->vptr_off  = ptr - ptr_start;
                    ~ ~~~~^~~~~~~~~~~
htslib/vcf.c:2426:26: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    info->vptr_len = ptr - info->vptr;
                   ~ ~~~~^~~~~~~~~~~~
htslib/vcf.c:2446:33: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        b->unpack_size[0] = ptr - ptr_ori;
                          ~ ~~~~^~~~~~~~~
htslib/vcf.c:2448:38: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        d->id = tmp.s; d->m_id = tmp.m;
                               ~ ~~~~^
htslib/vcf.c:2451:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand(char*, b->n_allele, d->m_allele, d->allele); // NM: hts_expand() is a macro
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:2460:33: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        b->unpack_size[1] = ptr - ptr_ori;
                          ~ ~~~~^~~~~~~~~
htslib/vcf.c:2461:40: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        d->als = tmp.s; d->m_als = tmp.m;
                                 ~ ~~~~^
htslib/vcf.c:2473:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            hts_expand(int, d->n_flt, d->m_flt, d->flt);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:2477:33: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        b->unpack_size[2] = ptr - ptr_ori;
                          ~ ~~~~^~~~~~~~~
htslib/vcf.c:2482:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand(bcf_info_t, b->n_info, d->m_info, d->info);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:2490:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand(bcf_fmt_t, b->n_fmt, d->m_fmt, d->fmt);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:2608:15: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        ret = bgzf_write(fp->fp.bgzf, line->s, line->l);
            ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:2610:15: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        ret = hwrite(fp->fp.hfile, line->s, line->l);
            ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:2621:15: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        ret = bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l);
            ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:2623:15: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        ret = hwrite(fp->fp.hfile, fp->line.s, fp->line.l);
            ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:2960:37: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
            uint32_t vptr_off = str.l;
                     ~~~~~~~~   ~~~~^
htslib/vcf.c:2993:34: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
            uint32_t p_off = str.l;
                     ~~~~~   ~~~~^
htslib/vcf.c:3044:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        kputsn(htxt.s, p - htxt.s, &str);
        ~~~~~~         ~~^~~~~~~~
htslib/vcf.c:3061:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    } else kputsn(htxt.s, htxt.l, &str);
           ~~~~~~         ~~~~~^
htslib/vcf.c:3210:25: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        var->n = (a-alt)-(r-ref); var->type = VCF_INDEL; return;
               ~ ~~~~~~~^~~~~~~~
htslib/vcf.c:3215:25: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        var->n = (a-alt)-(r-ref); var->type = VCF_INDEL; return;
               ~ ~~~~~~~^~~~~~~~
htslib/vcf.c:3229:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        var->n = -(re-r);
               ~ ^~~~~~~
htslib/vcf.c:3235:20: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        var->n = ae-a;
               ~ ~~^~
htslib/vcf.c:3241:32: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    var->n = ( re-r > ae-a ) ? -(re-r+1) : ae-a+1;
           ~                   ^~~~~~~~~
htslib/vcf.c:3241:48: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    var->n = ( re-r > ae-a ) ? -(re-r+1) : ae-a+1;
           ~                               ~~~~^~
htslib/vcf.c:3290:43: warning: implicit conversion loses integer precision: 'unsigned long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
            line->rlen = line->n_allele ? strlen(line->d.allele[0]) : 0;
                       ~                  ^~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:3318:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
            bcf_enc_vchar(&str, strlen((char*)values), (char*)values);
            ~~~~~~~~~~~~~       ^~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:3352:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand0(bcf_info_t, line->n_info, line->d.m_info , line->d.info);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:3372:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        int len = strlen(values[i]);
            ~~~   ^~~~~~~~~~~~~~~~~
htslib/vcf.c:3451:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        hts_expand0(bcf_fmt_t, line->n_fmt, line->d.m_fmt, line->d.fmt);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:115:19: note: expanded from macro 'hts_expand0'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:3499:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(int, line->d.n_flt, line->d.m_flt, line->d.flt);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:3520:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(int, line->d.n_flt, line->d.m_flt, line->d.flt);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:3558:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    hts_expand(char*, line->n_allele, line->d.m_allele, line->d.allele);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:86:19: note: expanded from macro 'hts_expand'
            (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
                ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:3572:46: warning: implicit conversion loses integer precision: 'unsigned long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    line->rlen = end_info ? end_info->v1.i : strlen(line->d.allele[0]);
               ~                             ^~~~~~~~~~~~~~~~~~~~~~~~~
htslib/vcf.c:3598:46: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    line->d.als = tmp.s; line->d.m_als = tmp.m;
                                       ~ ~~~~^
htslib/vcf.c:3608:46: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    line->d.als = tmp.s; line->d.m_als = tmp.m;
                                       ~ ~~~~^
htslib/vcf.c:3628:44: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    line->d.id = tmp.s; line->d.m_id = tmp.m;
                                     ~ ~~~~^
htslib/vcf.c:3640:15: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    int len = strlen(id);
        ~~~   ^~~~~~~~~~
htslib/vcf.c:3655:44: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    line->d.id = tmp.s; line->d.m_id = tmp.m;
                                     ~ ~~~~^
86 warnings generated.
In file included from htslib/vcf.c:38:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf.h:39:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/vcfutils.c -o build/temp.macosx-10.13-intel-2.7/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/vcfutils.c:27:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcfutils.h:29:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf.h:39:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/vcfutils.c:27:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcfutils.h:29:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf.h:40:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
htslib/vcfutils.c:328:33: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                    kputsn(ss,se-ss,&str);
                    ~~~~~~    ~~^~~
htslib/vcfutils.c:357:37: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                        kputsn(ss,se-ss,&str);
                        ~~~~~~    ~~^~~
htslib/vcfutils.c:372:112: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            nret = bcf_update_info(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void*)str.s, str.l, type);
                   ~~~~~~~~~~~~~~~                                                                         ~~~~^
htslib/vcfutils.c:572:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                    int k_src = 0, k_dst = 0, l = str.l;
                                              ~   ~~~~^
htslib/vcfutils.c:583:38: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                        kputsn(ss,ptr-ss,&str);
                        ~~~~~~    ~~~^~~
htslib/vcfutils.c:594:31: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                    l = str.l - l;
                      ~ ~~~~~~^~~
htslib/vcfutils.c:603:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                    int k_src = 0, k_dst = 0, l = str.l;
                                              ~   ~~~~^
htslib/vcfutils.c:635:46: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                kputsn(ss,ptr-ss,&str);
                                ~~~~~~    ~~~^~~
htslib/vcfutils.c:654:42: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                            kputsn(ss,ptr-ss,&str);
                            ~~~~~~    ~~~^~~
htslib/vcfutils.c:664:35: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                        l = str.l - l;
                          ~ ~~~~~~^~~
htslib/vcfutils.c:669:112: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            nret = bcf_update_format(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void*)str.s, str.l, type);
                   ~~~~~~~~~~~~~~~~~                                                                       ~~~~^
13 warnings generated.
In file included from htslib/vcfutils.c:27:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcfutils.h:29:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/vcf.h:39:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
1 warning generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.macosx-10.13-intel-2.7/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/cram/cram_codecs.c:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:61:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/cram/cram_codecs.c:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:77:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/sam_header.h:56:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from htslib/cram/cram_codecs.c:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/cram/cram_codecs.c:463:30: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    len += itf8_put_blk(b, tp-tmp);
           ~~~~~~~~~~~~    ~~^~~~
htslib/cram/cram_codecs.c:489:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    c->e_external.content_id = (size_t)dat;
                             ~ ^~~~~~~~~~~
htslib/cram/cram_codecs.c:1254:30: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    len += itf8_put_blk(b, tp-tmp);
           ~~~~~~~~~~~~    ~~^~~~
htslib/cram/cram_codecs.c:1657:20: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    *out_size = cp - (char *)(b->data + b->idx);
              ~ ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_codecs.c:1658:35: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    b->idx = cp - (char *)b->data + 1;
           ~ ~~~~~~~~~~~~~~~~~~~~~^~~
htslib/cram/cram_codecs.c:1697:20: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    *out_size = cp - (char *)(b->data + b->idx);
              ~ ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_codecs.c:1698:35: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    b->idx = cp - (char *)b->data + 1;
           ~ ~~~~~~~~~~~~~~~~~~~~~^~~
13 warnings generated.
In file included from htslib/cram/cram_codecs.c:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:61:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/cram/cram_codecs.c:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
5 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.macosx-10.13-intel-2.7/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/cram/cram_decode.c:49:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:61:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/cram/cram_decode.c:49:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:77:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/sam_header.h:56:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from htslib/cram/cram_decode.c:49:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/cram/cram_decode.c:83:12: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        return cp - op;
        ~~~~~~ ~~~^~~~
htslib/cram/cram_decode.c:93:13: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    sz = cp - op;
       ~ ~~~^~~~
htslib/cram/cram_decode.c:371:19: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        m->offset   = cp - (char *)b->data;
                    ~ ~~~^~~~~~~~~~~~~~~~~
htslib/cram/cram_decode.c:645:19: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        m->offset   = cp - (char *)b->data;
                    ~ ~~~^~~~~~~~~~~~~~~~~
htslib/cram/cram_decode.c:1226:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        orig_aux = BLOCK_SIZE(s->aux_blk);
                 ~ ^~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_decode.c:1925:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    cr->aux = BLOCK_SIZE(s->aux_blk);
            ~ ^~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_decode.c:1981:35: warning: implicit conversion loses integer precision: 'unsigned long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    cr->ntags = strlen((char *)TN)/3; // optimise to remove strlen
              ~ ~~~~~~~~~~~~~~~~~~^~
htslib/cram/cram_decode.c:1985:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    cr->aux = BLOCK_SIZE(s->aux_blk);
            ~ ^~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_decode.c:2309:42: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                s->ref_end = fd->refs->ref_id[ref_id]->length;
                           ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
htslib/cram/cram_decode.c:2458:50: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                    s->ref_end = fd->refs->ref_id[cr->ref_id]->length;
                               ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
htslib/cram/cram_decode.c:2518:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
            cr->name = BLOCK_SIZE(s->name_blk);
                     ~ ^~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_decode.c:2560:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
                cr->name = BLOCK_SIZE(s->name_blk);
                         ~ ^~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_decode.c:2650:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
            cr->seq = BLOCK_SIZE(s->seqs_blk);
                    ~ ^~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_decode.c:2658:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
            cr->qual = BLOCK_SIZE(s->qual_blk);
                     ~ ^~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_decode.c:2842:17: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
            name_len = strlen(fd->prefix);
                     ~ ^~~~~~~~~~~~~~~~~~
htslib/cram/cram_decode.c:2854:22: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            name_len = name - name_a;
                     ~ ~~~~~^~~~~~~~
htslib/cram/cram_decode.c:2919:20: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    return bam_idx + (aux - aux_orig);
    ~~~~~~ ~~~~~~~~^~~~~~~~~~~~~~~~~~
23 warnings generated.
In file included from htslib/cram/cram_decode.c:49:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:61:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/cram/cram_decode.c:49:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/cram/cram_decode.c:2309:42: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                s->ref_end = fd->refs->ref_id[ref_id]->length;
                           ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
htslib/cram/cram_decode.c:2458:50: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                    s->ref_end = fd->refs->ref_id[cr->ref_id]->length;
                               ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
7 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.macosx-10.13-intel-2.7/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/cram/cram_encode.c:43:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:61:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/cram/cram_encode.c:43:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:77:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/sam_header.h:56:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from htslib/cram/cram_encode.c:43:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/cram/cram_encode.c:234:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                itf8_put_blk(map, BLOCK_SIZE(h->TD_blk));
                ~~~~~~~~~~~~      ^~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_encode.c:249:38: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc));
    ~~~~~~~~~~~~     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
htslib/cram/cram_encode.c:450:38: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc));
    ~~~~~~~~~~~~     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
htslib/cram/cram_encode.c:498:38: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc));
    ~~~~~~~~~~~~     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
htslib/cram/cram_encode.c:504:5: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    BLOCK_UPLEN(cb);
    ^~~~~~~~~~~~~~~
htslib/cram/cram_io.h:614:41: note: expanded from macro 'BLOCK_UPLEN'
    (b)->comp_size = (b)->uncomp_size = BLOCK_SIZE((b))
                                      ~ ^~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_encode.c:537:29: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
        cp += itf8_put(cp, s->hdr->record_counter);
              ~~~~~~~~     ~~~~~~~~^~~~~~~~~~~~~~
htslib/cram/cram_encode.c:555:39: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    b->comp_size = b->uncomp_size = cp-buf;
                                  ~ ~~^~~~
htslib/cram/cram_encode.c:1034:50: warning: implicit conversion loses integer precision: 'unsigned long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    s->block[0]->uncomp_size = s->block[0]->byte + (s->block[0]->bit < 7);
                             ~ ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_encode.c:1049:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
            BLOCK_UPLEN(s->block[id]);
            ^~~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:614:41: note: expanded from macro 'BLOCK_UPLEN'
    (b)->comp_size = (b)->uncomp_size = BLOCK_SIZE((b))
                                      ~ ^~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_encode.c:1095:10: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        int n = bam_aux2i(TC);
            ~   ^~~~~~~~~~~~~
htslib/cram/cram_encode.c:1159:8: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
        u.e = e; u.c = 1;
            ~ ^
htslib/cram/cram_encode.c:1233:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
        cr->name        = BLOCK_SIZE(s->name_blk);
                        ~ ^~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_encode.c:1285:54: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
            c->ref_end   = fd->refs->ref_id[c->ref_seq_id]->length;
                         ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
htslib/cram/cram_encode.c:1331:55: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                    c->ref_end   = fd->refs->ref_id[c->ref_seq_id]->length;
                                 ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
htslib/cram/cram_encode.c:1801:24: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    f.b.seq_idx = base - (char *)BLOCK_DATA(s->seqs_blk);
                ~ ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_encode.c:1851:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        f.S.seq_idx = BLOCK_SIZE(s->base_blk);
                    ~ ^~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_encode.c:1858:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        f.S.seq_idx = BLOCK_SIZE(s->soft_blk);
                    ~ ^~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_encode.c:1918:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        f.S.seq_idx = BLOCK_SIZE(s->base_blk);
                    ~ ^~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_encode.c:1939:36: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    int aux_size = bam_blk_size(b) -
        ~~~~~~~~   ~~~~~~~~~~~~~~~~^
htslib/cram/cram_encode.c:2059:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    cr->aux = BLOCK_SIZE(s->aux_blk);
            ~ ^~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_encode.c:2060:30: warning: implicit conversion loses integer precision: 'long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    cr->aux_size = (uc *)tmp - (BLOCK_DATA(s->aux_blk) + cr->aux);
                 ~ ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_encode.c:2079:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int TD_blk_size = BLOCK_SIZE(td_b), new;
        ~~~~~~~~~~~   ^~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_encode.c:2317:38: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                codec->encode(s, codec, aux_s, aux - aux_s);
                ~~~~~                          ~~~~^~~~~~~
htslib/cram/cram_encode.c:2583:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    cr->seq         = BLOCK_SIZE(s->seqs_blk);
                    ~ ^~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_encode.c:2584:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
    cr->qual        = BLOCK_SIZE(s->qual_blk);
                    ~ ^~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
31 warnings generated.
In file included from htslib/cram/cram_encode.c:43:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:61:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/cram/cram_encode.c:43:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/cram/cram_encode.c:537:29: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
        cp += itf8_put(cp, s->hdr->record_counter);
              ~~~~~~~~     ~~~~~~~~^~~~~~~~~~~~~~
htslib/cram/cram_encode.c:1095:10: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        int n = bam_aux2i(TC);
            ~   ^~~~~~~~~~~~~
htslib/cram/cram_encode.c:1159:8: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
        u.e = e; u.c = 1;
            ~ ^
htslib/cram/cram_encode.c:1285:54: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
            c->ref_end   = fd->refs->ref_id[c->ref_seq_id]->length;
                         ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
htslib/cram/cram_encode.c:1331:55: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                    c->ref_end   = fd->refs->ref_id[c->ref_seq_id]->length;
                                 ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
10 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/cram/cram_external.c -o build/temp.macosx-10.13-intel-2.7/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/cram/cram_external.c:44:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:61:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/cram/cram_external.c:44:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:77:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/sam_header.h:56:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from htslib/cram/cram_external.c:44:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/cram/cram_external.c:200:60: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
int32_t cram_block_get_size(cram_block *b)        { return BLOCK_SIZE(b); }
                                                    ~~~~~~ ^~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
htslib/cram/cram_external.c:216:46: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
void cram_block_update_size(cram_block *b) { BLOCK_UPLEN(b); }
                                             ^~~~~~~~~~~~~~
htslib/cram/cram_io.h:614:41: note: expanded from macro 'BLOCK_UPLEN'
    (b)->comp_size = (b)->uncomp_size = BLOCK_SIZE((b))
                                      ~ ^~~~~~~~~~~~~~~
htslib/cram/cram_io.h:494:29: note: expanded from macro 'BLOCK_SIZE'
#define BLOCK_SIZE(b) ((b)->byte)
                       ~~~~~^~~~
8 warnings generated.
In file included from htslib/cram/cram_external.c:44:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:45:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram_samtools.h:61:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/sam.h:31:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/cram/cram_external.c:44:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
5 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.macosx-10.13-intel-2.7/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from htslib/cram/cram_index.c:65:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/cram/cram_index.c:65:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:31:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/textutils_internal.h:32:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/kstring.h:156:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        return kputsn(p, strlen(p), s);
               ~~~~~~    ^~~~~~~~~
In file included from htslib/cram/cram_index.c:66:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
htslib/cram/cram_index.c:184:18: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
        if (kputsn(buf, len, &kstr) < 0)
            ~~~~~~      ^~~
7 warnings generated.
In file included from htslib/cram/cram_index.c:65:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/hts_internal.h:29:
/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/htslib/hts.h:783:40: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
        if (beg>>s == end>>s) return t + (beg>>s);
                              ~~~~~~ ~~^~~~~~~~~~
In file included from htslib/cram/cram_index.c:66:
In file included from /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib/cram/cram.h:48:
htslib/cram/cram_io.h:599:27: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        return append_uint32(cp, i);
               ~~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:602:26: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, j/1000000000);
             ~~~~~~~~~~~~~     ~^~~~~~~~~~~
htslib/cram/cram_io.h:604:24: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_sub32(cp, j);
             ~~~~~~~~~~~~     ^
htslib/cram/cram_io.h:606:27: warning: implicit conversion loses integer precision: 'unsigned long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        cp = append_uint32(cp, i / 1000000000);
             ~~~~~~~~~~~~~     ~~^~~~~~~~~~~~
5 warnings generated.
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/htslib -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/samtools/lz4 -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/bcftools -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/pysam -I/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.macosx-10.13-intel-2.7/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
htslib/cram/cram_io.c:63:10: fatal error: 'os/lzma_stub.h' file not found
#include "os/lzma_stub.h"
         ^~~~~~~~~~~~~~~~
1 error generated.
error: command 'cc' failed with exit status 1

----------------------------------------

Command "/usr/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-record-ni9iS8/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/bf/b3ybbc1545l22qmp93gj0cph0000gp/T/pip-install-Dx99Af/pysam/

AndreasHeger commented 6 years ago

Hi, is it possible for you to install via conda? This will take care of most of the dependencies.

krat19 commented 6 years ago

Yes. Thanks for your reply. I actually tried that and it works. Sorry for not updating you sooner. Much appreciated!

Sent from my iPhone

On Jul 27, 2018, at 12:44 PM, Andreas Heger notifications@github.com wrote:

Hi, is it possible for you to install via conda? This will take care of most of the dependencies.

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