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Adding option to mergeSTR to give file with list of VCFs #204

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merged 3 commits into from
Jan 4, 2024

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gymreklab
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Currently mergeSTR requires the argument --vcf which takes a comma-separated list of VCF files to merge. When running mergeSTR on a large number of files, this results in very long commands. This PR adds the option --vcfs-list to mergeSTR as an alternative which allows users to specify a file with a list of the VCFs to merge (one file per line).

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@aryarm aryarm left a comment

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looks good! I made a small suggestion for the test

also, we should remember to list this change in the CHANGELOG.md file once we merge #201

trtools/mergeSTR/tests/test_mergeSTR.py Outdated Show resolved Hide resolved
@gymreklab gymreklab merged commit 21c94e4 into master Jan 4, 2024
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@aryarm aryarm deleted the mergestr-filelist branch January 4, 2024 00:24
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