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HTTP request sent, awaiting response... 302 Found Location: https://github-repository-files.githubusercontent.com/11368595/6271998?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210412%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210412T212409Z&X-Amz-Expires=300&X-Amz-Signature=abfddde31fc5a72667047c1ceeb139f0f3fc6d9c50ba65603a07b6fd2d706587&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=11368595&response-content-disposition=attachment%3Bfilename%3DNC_045512.2.fasta.txt&response-content-type=text%2Fplain [following] --2021-04-12 23:24:09-- https://github-repository-files.githubusercontent.com/11368595/6271998?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210412%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210412T212409Z&X-Amz-Expires=300&X-Amz-Signature=abfddde31fc5a72667047c1ceeb139f0f3fc6d9c50ba65603a07b6fd2d706587&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=11368595&response-content-disposition=attachment%3Bfilename%3DNC_045512.2.fasta.txt&response-content-type=text%2Fplain Resolving github-repository-files.githubusercontent.com (github-repository-files.githubusercontent.com)... 185.199.109.154, 185.199.111.154, 185.199.110.154, ... Connecting to github-repository-files.githubusercontent.com (github-repository-files.githubusercontent.com)|185.199.109.154|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 30417 (30K) [text/plain] Saving to: ‘NC_045512.2.fasta.txt’ 0K .......... .......... ......... 100% 6.87M=0.004s 2021-04-12 23:24:09 (6.87 MB/s) - ‘NC_045512.2.fasta.txt’ saved [30417/30417] --2021-04-12 23:24:09-- https://github.com/samtools/bcftools/releases/download/1.12/bcftools-1.12.tar.bz2 Resolving github.com (github.com)... 140.82.121.4 Connecting to github.com (github.com)|140.82.121.4|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://github-releases.githubusercontent.com/11368595/2f1eca80-8707-11eb-9fcf-a4ab114e8614?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210412%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210412T212409Z&X-Amz-Expires=300&X-Amz-Signature=550b3dd6934202bebd26167970869603b260dd8183bda7a2e27dc10135abda49&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=11368595&response-content-disposition=attachment%3B%20filename%3Dbcftools-1.12.tar.bz2&response-content-type=application%2Foctet-stream [following] --2021-04-12 23:24:09-- https://github-releases.githubusercontent.com/11368595/2f1eca80-8707-11eb-9fcf-a4ab114e8614?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210412%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210412T212409Z&X-Amz-Expires=300&X-Amz-Signature=550b3dd6934202bebd26167970869603b260dd8183bda7a2e27dc10135abda49&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=11368595&response-content-disposition=attachment%3B%20filename%3Dbcftools-1.12.tar.bz2&response-content-type=application%2Foctet-stream Resolving github-releases.githubusercontent.com (github-releases.githubusercontent.com)... 185.199.110.154, 185.199.111.154, 185.199.108.154, ... 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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 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 location of HTSlib source tree... htslib-1.12 checking shared library type... Darwin dylib checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h === configuring in htslib-1.12 (/tmp/bar/bcftools-1.12/htslib-1.12) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' 'LDFLAGS=-L/usr/local/opt/lapack/lib' 'CPPFLAGS=-I/usr/local/opt/lapack/include' --cache-file=/dev/null --srcdir=. 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 pkg-config... /usr/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Darwin... Darwin dylib checking whether the compiler accepts -fvisibility=hidden... yes 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 for srand48_deterministic... no 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... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl_easy_pause in -lcurl... yes checking for CCHmac... yes checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htscodecs.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.mk:59: htslib-1.12/htslib_static.mk: No such file or directory cd htslib-1.12 && /Library/Developer/CommandLineTools/usr/bin/make htslib_static.mk sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk echo '#define BCFTOOLS_VERSION "1.12"' > version.h gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o main.o main.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o tabix.o tabix.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o filter.o filter.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o mcall.o mcall.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o reheader.o reheader.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o convert.o convert.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o HMM.o HMM.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o consensus.o consensus.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o bin.o bin.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o hclust.o hclust.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o version.o version.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o regidx.o regidx.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o csq.o csq.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o cols.o cols.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o extsort.o extsort.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o dist.o dist.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o abuf.o abuf.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o ccall.o ccall.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o em.o em.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o prob1.o prob1.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o kmin.o kmin.c gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -DPLUGINPATH='"/usr/local/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c cd htslib-1.12 && /Library/Developer/CommandLineTools/usr/bin/make hts-object-files gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o kfunc.o kfunc.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o kstring.o kstring.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o bgzf.o bgzf.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o errmod.o errmod.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o faidx.o faidx.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o header.o header.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.12"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h echo '#define HTS_CPPFLAGS "-I/usr/local/opt/lapack/include"' >> config_vars.h echo '#define HTS_CFLAGS "-Wall -g -O2 -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LDFLAGS "-L/usr/local/opt/lapack/lib -fvisibility=hidden "' >> config_vars.h echo '#define HTS_LIBS "-llzma -lbz2 -lz -lcurl "' >> config_vars.h gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o hts.o hts.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o hts_expr.o hts_expr.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o hts_os.o hts_os.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o md5.o md5.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o multipart.o multipart.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o probaln.o probaln.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o realn.o realn.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o regidx.o regidx.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o region.o region.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o sam.o sam.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o vcf_sweep.o vcf_sweep.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o tbx.o tbx.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o textutils.o textutils.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o thread_pool.o thread_pool.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o vcf.o vcf.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o vcfutils.o vcfutils.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/cram_decode.o cram/cram_decode.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/cram_encode.o cram/cram_encode.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/cram_external.o cram/cram_external.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/cram_index.o cram/cram_index.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/cram_io.o cram/cram_io.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/cram_stats.o cram/cram_stats.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/mFILE.o cram/mFILE.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o cram/string_alloc.o cram/string_alloc.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o hfile_libcurl.o hfile_libcurl.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o hfile_gcs.o hfile_gcs.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o hfile_s3.o hfile_s3.c gcc -Wall -g -O2 -fvisibility=hidden -I. -I/usr/local/opt/lapack/include -c -o hfile_s3_write.o hfile_s3_write.c touch hts-object-files cd htslib-1.12 && /Library/Developer/CommandLineTools/usr/bin/make lib-static ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o ranlib libhts.a gcc -rdynamic -L/usr/local/opt/lapack/lib -L/usr/local/opt/lapack/lib -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o vcfplugin.o htslib-1.12/libhts.a -lpthread -lz -lm -lbz2 -llzma -lcurl -lm -lz -lpthread gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o test/test-rbuf.o test/test-rbuf.c gcc -L/usr/local/opt/lapack/lib -o test/test-rbuf test/test-rbuf.o -lz gcc -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -c -o test/test-regidx.o test/test-regidx.c gcc -L/usr/local/opt/lapack/lib -L/usr/local/opt/lapack/lib -o test/test-regidx test/test-regidx.o regidx.o htslib-1.12/libhts.a -lpthread -lz -lm -lbz2 -llzma -lcurl -lpthread -lz gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/GTisec.so version.c plugins/GTisec.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/allele-length.so version.c plugins/allele-length.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/contrast.so version.c plugins/contrast.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/counts.so version.c plugins/counts.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/dosage.so version.c plugins/dosage.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/fixref.so version.c plugins/fixref.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/impute-info.so version.c plugins/impute-info.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/mendelian.so version.c plugins/mendelian.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/prune.so version.c plugins/prune.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/scatter.so version.c plugins/scatter.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/setGT.so version.c plugins/setGT.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/split-vep.so version.c plugins/split-vep.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/split.so version.c plugins/split.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup -Wall -g -O2 -I. -Ihtslib-1.12 -I/usr/local/opt/lapack/include -L/usr/local/opt/lapack/lib -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c bcftools 1.12 Using htslib 1.12 Copyright (C) 2021 Genome Research Ltd. License Expat: The MIT/Expat license This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 1000000 NC_045512.2 4253 . C T 222.391 . DP=1531;AD=360,406;VDB=0;SGB=-0.693147;RPB=0.984628;MQB=1;MQSB=1;BQB=0.911924;MQ0F=0;AC=1;AN=2;DP4=359,1,406,0;MQ=60 GT:PL 0/1:255,0,255