grenaud
commented
2 years ago That is strange. It seems to be working for me:
gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o amplicon_stats.o amplicon_stats.c
gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o bam_import.o bam_import.c
gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o bam_samples.o bam_samples.c
gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o lz4/lz4.o lz4/lz4.c
gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o sam_opts.o sam_opts.c
gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o sam_utils.o sam_utils.c
gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o bedidx.o bedidx.c
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o
Can you build samtools? If not, please go to their github and report the issue.
pengyan19
hello, i want to install this software,but i meet this question as follows,please help me to solved its.
bam_ampliconclip.c: In function ‘amplicon_clip_main’: bam_ampliconclip.c:639:23: warning: ‘sites’ may be used uninitialized in this function [-Wmaybe-uninitialized] bed_entry_list_t *sites; ^ gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o amplicon_stats.o amplicon_stats.c gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o bam_import.o bam_import.c bam_import.c: In function ‘import_fastq’: bam_import.c:180:35: error: ‘FASTQ_OPT_NAME2’ undeclared (first use in this function) hts_set_opt(fp_in[i], FASTQ_OPT_NAME2, 1); ^ bam_import.c:180:35: note: each undeclared identifier is reported only once for each function it appears in make[1]: [Makefile:138: bam_import.o] Error 1 make[1]: Leaving directory '/home/pengyan/biosoft/glactools-master/samtools' make: [Makefile:47: samtools/libbam.a] Error 2