What container were you trying to use, and how were you attempting to use it?
The bcftools Dockerfile results in a bcftools executable that is missing several useful features, and slower to compress output as well.
bcftools has many compile time options that will be enabled upon running ./configure, but the default makefile is very conservative and does not enable them. For example, my group tried to use this docker image to read directly from Google Cloud Storage, and discovered that the feature is not enabled.
bcftools, samtools, and htslib have recommended using libdeflate instead of zlib, as this can double compression and decompression speed: https://www.htslib.org/benchmarks/zlib.html
Running configure before building bcftools will enable GCS, S3, and libdeflate support, resolving this issue.
Relevant log output
The default config.h that we are building htslib with:
/* Default config.h generated by Makefile */
#ifndef _XOPEN_SOURCE
#define _XOPEN_SOURCE 600
#endif
#define HAVE_LIBBZ2 1
#define HAVE_LIBLZMA 1
#ifndef __APPLE__
#define HAVE_LZMA_H 1
#endif
#define HAVE_DRAND48 1
#define HAVE_LIBCURL 1
#define HAVE_POPCNT 1
#define HAVE_SSE4_1 1
#define HAVE_SSSE3 1
#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0
#define UBSAN 1
#endif
#define HAVE_AVX2 1
#define HAVE_AVX512 1
config.h after running ./configure:
/* config.h. Generated from config.h.in by configure. */
/* config.h.in. Generated from configure.ac by autoheader. */
/* If you use configure, this file provides #defines reflecting your
configuration choices. If you have not run configure, suitable
conservative defaults will be used.
Autoheader adds a number of items to this template file that are not
used by HTSlib: STDC_HEADERS and most HAVE_*_H header file defines
are immaterial, as we assume standard ISO C headers and facilities;
the PACKAGE_* defines are unused and are overridden by the more
accurate PACKAGE_VERSION as computed by the Makefile. */
/* Define if HTSlib should enable GCS support. */
#define ENABLE_GCS 1
/* Define if HTSlib should enable plugins. */
/* #undef ENABLE_PLUGINS */
/* Define if HTSlib should enable S3 support. */
#define ENABLE_S3 1
/* Defined to 1 if rANS source using AVX2 can be compiled. */
#define HAVE_AVX2 1
/* Defined to 1 if rANS source using AVX512F can be compiled. */
#define HAVE_AVX512 1
/* Define if you have the Common Crypto library. */
#define HAVE_COMMONCRYPTO 1
/* Define to 1 if you have the 'drand48' function. */
#define HAVE_DRAND48 1
/* Define if using an external libhtscodecs */
/* #undef HAVE_EXTERNAL_LIBHTSCODECS */
/* Define to 1 if you have the 'fdatasync' function. */
/* #undef HAVE_FDATASYNC */
/* Define to 1 if you have the 'fsync' function. */
#define HAVE_FSYNC 1
/* Define to 1 if you have the 'getpagesize' function. */
#define HAVE_GETPAGESIZE 1
/* Define to 1 if you have the 'gmtime_r' function. */
#define HAVE_GMTIME_R 1
/* Define if you have libcrypto-style HMAC(). */
/* #undef HAVE_HMAC */
/* Define to 1 if you have the <inttypes.h> header file. */
#define HAVE_INTTYPES_H 1
/* Define to 1 if you have the 'bz2' library (-lbz2). */
#define HAVE_LIBBZ2 1
/* Define if libcurl file access is enabled. */
#define HAVE_LIBCURL 1
/* Define if libdeflate is available. */
#define HAVE_LIBDEFLATE 1
/* Define to 1 if you have the 'lzma' library (-llzma). */
#define HAVE_LIBLZMA 1
/* Define to 1 if you have the 'z' library (-lz). */
#define HAVE_LIBZ 1
/* Define to 1 if you have the <lzma.h> header file. */
#define HAVE_LZMA_H 1
/* Define to 1 if you have a working 'mmap' system call. */
#define HAVE_MMAP 1
/* Defined to 1 if rANS source using popcnt can be compiled. */
#define HAVE_POPCNT 1
/* Define to 1 if you have the 'srand48_deterministic' function. */
/* #undef HAVE_SRAND48_DETERMINISTIC */
/* Defined to 1 if rANS source using SSE4.1 can be compiled. */
#define HAVE_SSE4_1 1
/* Defined to 1 if rANS source using SSSE3 can be compiled. */
#define HAVE_SSSE3 1
/* Define to 1 if you have the <stdint.h> header file. */
#define HAVE_STDINT_H 1
/* Define to 1 if you have the <stdio.h> header file. */
#define HAVE_STDIO_H 1
/* Define to 1 if you have the <stdlib.h> header file. */
#define HAVE_STDLIB_H 1
/* Define to 1 if you have the <strings.h> header file. */
#define HAVE_STRINGS_H 1
/* Define to 1 if you have the <string.h> header file. */
#define HAVE_STRING_H 1
/* Define to 1 if you have the <sys/param.h> header file. */
#define HAVE_SYS_PARAM_H 1
/* Define to 1 if you have the <sys/stat.h> header file. */
#define HAVE_SYS_STAT_H 1
/* Define to 1 if you have the <sys/types.h> header file. */
#define HAVE_SYS_TYPES_H 1
/* Define to 1 if you have the <unistd.h> header file. */
#define HAVE_UNISTD_H 1
/* Define to the address where bug reports for this package should be sent. */
#define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net"
/* Define to the full name of this package. */
#define PACKAGE_NAME "HTSlib"
/* Define to the full name and version of this package. */
#define PACKAGE_STRING "HTSlib 1.20"
/* Define to the one symbol short name of this package. */
#define PACKAGE_TARNAME "htslib"
/* Define to the home page for this package. */
#define PACKAGE_URL "http://www.htslib.org/"
/* Define to the version of this package. */
#define PACKAGE_VERSION "1.20"
/* Platform-dependent plugin filename extension. */
/* #undef PLUGIN_EXT */
/* Define to 1 if all of the C89 standard headers exist (not just the ones
required in a freestanding environment). This macro is provided for
backward compatibility; new code need not use it. */
#define STDC_HEADERS 1
/* Prevent unaligned access in htscodecs SSE4 rANS codec */
#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0
#define UBSAN 1
#endif
/* Number of bits in a file offset, on hosts where this is settable. */
/* #undef _FILE_OFFSET_BITS */
/* Define to 1 on platforms where this makes off_t a 64-bit type. */
/* #undef _LARGE_FILES */
/* Number of bits in time_t, on hosts where this is settable. */
/* #undef _TIME_BITS */
/* Specify X/Open requirements */
#define _XOPEN_SOURCE 600
/* Define to 1 on platforms where this makes time_t a 64-bit type. */
/* #undef __MINGW_USE_VC2005_COMPAT */
What container were you trying to use, and how were you attempting to use it?
The bcftools Dockerfile results in a bcftools executable that is missing several useful features, and slower to compress output as well.
bcftools has many compile time options that will be enabled upon running ./configure, but the default makefile is very conservative and does not enable them. For example, my group tried to use this docker image to read directly from Google Cloud Storage, and discovered that the feature is not enabled.
bcftools, samtools, and htslib have recommended using libdeflate instead of zlib, as this can double compression and decompression speed: https://www.htslib.org/benchmarks/zlib.html
Running configure before building bcftools will enable GCS, S3, and libdeflate support, resolving this issue.
Relevant log output