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Fixed '--only' issue
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Harrison Deng 2023-06-27 20:20:59 +00:00
parent c25f4ab9a1
commit 9245b3f68e
3 changed files with 19 additions and 1 deletions
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1
.vscode/settings.json vendored
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@ -12,6 +12,7 @@
"cSpell.words": [ "cSpell.words": [
"bioconda", "bioconda",
"CHROM", "CHROM",
"modvcfsamples",
"pytest", "pytest",
"pyvcf", "pyvcf",
"vcfpy", "vcfpy",

17
out/test_files_shortened_haploid.vcf Normal file
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@ -0,0 +1,17 @@
##fileformat=VCFv4.1
##fileDate=10122015_22h01m13s
##source=SHAPEIT2.v837
##log_file=shapeit_10122015_22h01m13s_3f764d75-2fbb-42df-ab75-8c2dfd5731ce.log
##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Gambian Chinese French Brazilian Nigerian Pakistani English Colombian Indian Japanese
1 846808 rs4475691 C T 100 . AC=1276;AN=5008;DP=20368 GT:GQ:DP 1|1|1|1:70:60 0|0|0|0:30:10 0|0|0|0:20:40 ./.:0:0 0|0|0|0:70:60 0|0|0|0:90:30 0|0|0|0:80:70 0|0|0|0:50:80 ./.:0:0 0|0|0|0:100:80
1 846854 rs111957712 G A 100 . AC=114;AN=5008;DP=20538 GT:GQ:DP ./.:0:0 0|0|0|0:40:30 0|0|0|0:80:30 0|0|0|0:0:20 0|0|0|0:40:80 0|0|0|0:10:30 ./.:0:0 ./.:0:0 0|0|0|0:70:0 0|0|0|0:90:30
1 846864 rs950122 G C 100 . AC=1116;AN=5008;DP=20582 GT:GQ:DP 1|1|1|1:60:0 0|0|0|0:20:0 0|0|0|0:90:70 0|0|0|0:80:50 0|0|0|0:80:30 0|0|0|0:10:80 0|0|0|0:100:20 0|0|0|0:30:40 ./.:0:0 0|0|0|0:30:90
1 847228 rs3905286 C T 100 . AC=1215;AN=5008;DP=20731 GT:GQ:DP 1|1|1|1:70:80 0|0|0|0:90:80 0|0|0|0:60:50 0|0|0|0:60:90 0|0|0|0:30:40 0|0|0|0:70:10 0|0|0|0:100:80 0|0|0|0:100:50 0|0|0|0:70:100 0|0|0|0:40:40
1 847297 rs11507768 G A 100 . AC=359;AN=5008;DP=20809 GT:GQ:DP 1|1|1|1:0:60 0|0|0|0:10:30 0|0|0|0:80:60 ./.:0:0 0|0|0|0:10:100 0|0|0|0:10:100 ./.:0:0 0|0|0|0:100:40 0|0|0|0:20:20 0|0|0|0:10:0
1 847491 rs28407778 G A 100 . AC=1262;AN=5008;DP=16939 GT:GQ:DP 1|1|1|1:0:100 0|0|0|0:70:40 0|0|0|0:0:60 0|0|0|0:90:90 0|0|0|0:90:90 ./.:0:0 0|0|0|0:70:60 0|0|0|0:70:0 0|0|0|0:90:100 0|0|0|0:60:60
1 848023 rs144407116 C A 100 . AC=52;AN=5008;DP=22562 GT:GQ:DP 0|0|0|0:10:60 0|0|0|0:20:80 0|0|0|0:20:50 0|0|0|0:20:90 0|0|0|0:90:10 0|0|0|0:70:60 0|0|0|0:40:30 0|0|0|0:60:0 0|0|0|0:40:40 0|0|0|0:10:10
1 848090 rs4246505 G A 100 . AC=857;AN=5008;DP=19301 GT:GQ:DP 0|0|0|0:70:70 0|0|0|0:90:30 0|0|0|0:40:10 0|0|0|0:80:20 0|0|0|0:50:50 0|0|0|0:10:30 ./.:0:0 0|0|0|0:20:60 ./.:0:0 0|0|0|0:90:0
1 848445 rs4626817 G A 100 . AC=1255;AN=5008;DP=18444 GT:GQ:DP 1|1|1|1:100:40 0|0|0|0:80:90 0|0|0|0:30:100 0|0|0|0:100:60 0|0|0|0:40:90 0|0|0|0:20:30 0|0|0|0:70:100 ./.:0:0 ./.:0:0 0|0|0|0:80:30
1 848456 rs11507767 A G 100 . AC=1266;AN=5008;DP=18137 GT:GQ:DP 1|1|1|1:40:30 ./.:0:0 0|0|0|0:60:90 0|0|0|0:60:40 0|0|0|0:100:80 0|0|0|0:50:50 0|0|0|0:0:10 0|0|0|0:60:0 0|0|0|0:100:100 ./.:0:0
1 848738 rs3829741 C T 100 . AC=855;AN=5008;DP=16663 GT:GQ:DP 0|0|0|0:50:90 0|0|0|0:50:50 0|0|0|0:50:30 0|0|0|0:60:60 0|0|0|0:80:40 0|0|0|0:50:80 0|0|0|0:0:80 0|0|0|0:0:30 0|0|0|0:10:0 0|0|0|0:70:30

2
src/modvcfsamples/cli.py
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@ -8,7 +8,7 @@ def run(vcfs: list[str], only: list[str], gt: Union[int, None], output_dir: str)
vcf_records, header = sample.get_records_from_vcf(vcf) vcf_records, header = sample.get_records_from_vcf(vcf)
modified_vcfs = vcf_records modified_vcfs = vcf_records
modified_header = header modified_header = header
if len(only) > 1: if len(only) > 0:
modified_vcfs, modified_header = sample.keep_specific_call_data(modified_vcfs, modified_header, *only) modified_vcfs, modified_header = sample.keep_specific_call_data(modified_vcfs, modified_header, *only)
if gt is not None: if gt is not None:
modified_vcfs, modified_header = sample.normalize_gt_to_length(modified_vcfs, modified_header, gt) modified_vcfs, modified_header = sample.normalize_gt_to_length(modified_vcfs, modified_header, gt)