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Update BCFtools to use stable sort #1813

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Update BCFtools to use stable sort #1813

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a97a49d
update htslib/samtools/bcftools; use bcftools stable sort
ASLeonard Nov 3, 2025
2bc8dbd
fix missing bracket
ASLeonard Nov 3, 2025
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15 changes: 0 additions & 15 deletions build-tools/downloadMafTools
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Original file line number Diff line number Diff line change
Expand Up @@ -34,21 +34,6 @@ fi

# taffy
cd ${mafBuildDir}
wget -q https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
tar --no-same-owner -xf samtools-1.11.tar.bz2
cd samtools-1.11
SAMTOOLS_CONFIG_OPTS=""
if [[ $STATIC_CHECK -eq 1 ]]
then
SAMTOOLS_CONFIG_OPTS="--disable-shared --enable-static"
fi
./configure --without-curses --disable-libcurl --enable-configure-htslib $SAMTOOLS_CONFIG_OPTS
make -j ${numcpu}
cd htslib-1.11
make -j ${numcpu} libhts.a
export HTSLIB_CFLAGS=-I$(pwd)
export HTSLIB_LIBS="$(pwd)/libhts.a -lbz2 -ldeflate -lm -lpthread -lz -llzma -pthread -lpthread"
cd ${mafBuildDir}
git clone https://github.com/ComparativeGenomicsToolkit/taffy.git
cd taffy
git checkout 1329d999948ad4acc10116276fa7a9752a749595
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14 changes: 7 additions & 7 deletions build-tools/downloadPangenomeTools
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Expand Up @@ -89,9 +89,9 @@ fi

#samtools
cd ${pangenomeBuildDir}
wget -q https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
tar --no-same-owner -xf samtools-1.11.tar.bz2
cd samtools-1.11
wget -q https://github.com/samtools/samtools/releases/download/1.22.1/samtools-1.22.1.tar.bz2
tar --no-same-owner -xf samtools-1.22.1.tar.bz2
cd samtools-1.22.1
SAMTOOLS_CONFIG_OPTS=""
if [[ $STATIC_CHECK -eq 1 ]]
then
Expand All @@ -105,7 +105,7 @@ then
else
exit 1
fi
cd htslib-1.11
cd htslib-1.22.1
make -j ${numcpu} tabix
make -j ${numcpu} bgzip
if [[ $STATIC_CHECK -ne 1 || $(ldd tabix | grep so | wc -l) -eq 0 ]]
Expand All @@ -123,9 +123,9 @@ fi

#bcftools
cd ${pangenomeBuildDir}
wget -q https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.19.tar.bz2
tar --no-same-owner -xf bcftools-1.19.tar.bz2
cd bcftools-1.19
wget -q https://github.com/samtools/bcftools/releases/download/1.22/bcftools-1.22.tar.bz2
tar --no-same-owner -xf bcftools-1.22.tar.bz2
cd bcftools-1.22
SAMTOOLS_CONFIG_OPTS=""
if [[ $STATIC_CHECK -eq 1 ]]
then
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11 changes: 3 additions & 8 deletions src/cactus/refmap/cactus_graphmap_join.py
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Expand Up @@ -1213,15 +1213,13 @@ def vcfnorm(job, config, vcf_ref, vcf_id, vcf_path, tbi_id, fasta_ref_dict):
job.fileStore.readGlobalFile(fasta_ref_dict[vcf_ref], fa_ref_path)

norm_path = os.path.join(work_dir, 'norm.' + os.path.basename(vcf_path))
cactus_call(parameters=['bcftools', 'view', '-h', '-Oz', vcf_path], outfile=norm_path)
view_cmd = ['bcftools', 'view', '-H']
view_cmd = ['bcftools', 'view']
if getOptionalAttrib(findRequiredNode(config.xmlRoot, "graphmap_join"), "filterAC0", typeFn=bool, default=False):
view_cmd += ['-e', 'AC=0']
cactus_call(parameters=[['bcftools', 'norm', '-m', '-any', vcf_path],
['bcftools', 'norm', '-f', fa_ref_path],
view_cmd,
['sort', '-k1,1d', '-k2,2n', '-s', '-T', work_dir],
['bgzip']], outfile=norm_path, outappend=True)
['bcftools', 'sort', '-Oz', '-T', work_dir]], outfile=norm_path)
merge_duplicates_opts = getOptionalAttrib(findRequiredNode(config.xmlRoot, "graphmap_join"), "mergeDuplicatesOptions", typeFn=str, default=None)
if merge_duplicates_opts not in [None, "0"]:
#note: merge_duplcates complains about not having a .tbi but I don't think it actually affects anything
Expand Down Expand Up @@ -1493,10 +1491,7 @@ def vcf_cat(job, vcf_tbi_ids, tag, sort=False, fix_ploidies=True):
# stable sort, which is apparently not guaranteed by bcftools sort
# (this could be useful for merge_duplicates.py)
sort_vcf_path = os.path.join(work_dir, '{}sort.vcf.gz'.format(tag))
cactus_call(parameters=['bcftools', 'view', '-Oz', '-h', cat_vcf_path], outfile=sort_vcf_path)
cactus_call(parameters=[['bcftools', 'view', '-H', cat_vcf_path],
['sort', '-k1,1d', '-k2,2n', '-s', '-T', work_dir],
['bgzip']], outfile=sort_vcf_path, outappend=True)
cactus_call(parameters=['bcftools', 'sort', '-Oz', '-T', work_dir, cat_vcf_path], outfile=sort_vcf_path)
cat_vcf_path = sort_vcf_path

if fix_ploidies:
Expand Down