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add -a to bcftools concat #1809

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add -a to bcftools concat #1809

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758003a
add -a to bcftools concat
glennhickey Oct 30, 2025
ab0542e
try again to fix ci
glennhickey Oct 30, 2025
05def95
index before cat
glennhickey Oct 31, 2025
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ RUN cd /home/cactus && rm -rf cactus_env && \
. cactus_env/bin/activate && \
python3 -m pip install -U setuptools pip && \
python3 -m pip install -U -r ./toil-requirement.txt && \
python3 -m pip install -U .
python3 -m pip install -U --no-build-isolation .

# prep the hal python install which is not part of the setup
RUN rm -rf /home/cactus/hal_lib && \
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9 changes: 8 additions & 1 deletion src/cactus/refmap/cactus_graphmap_join.py
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Expand Up @@ -1476,9 +1476,16 @@ def vcf_cat(job, vcf_tbi_ids, tag, sort=False, fix_ploidies=True):
['bcftools', 'view', '-S', all_sample_list_path, '-O', 'z']],
outfile=updated_vcf_path)
vcf_paths[i] = updated_vcf_path

# -a below requires indexes
for vcf_path in vcf_paths:
try:
cactus_call(parameters=['tabix', '-fp', 'vcf', vcf_path])
except:
cactus_call(parameters=['bcftools', 'index', '-c', vcf_path])

cat_vcf_path = os.path.join(work_dir, '{}vcf.gz'.format(tag))
cactus_call(parameters=['bcftools', 'concat', '-O', 'z', '--threads', str(job.cores)] + \
cactus_call(parameters=['bcftools', 'concat', '-a', '-O', 'z', '--threads', str(job.cores)] + \
[os.path.basename(vcf_path) for vcf_path in vcf_paths],
work_dir=work_dir, outfile=cat_vcf_path)

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