Update wrapper script for paired WGS pipeline (battenberg_wgs.R)#174
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s-basrai wants to merge 5 commits into
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Update wrapper script for paired WGS pipeline (battenberg_wgs.R)#174s-basrai wants to merge 5 commits into
s-basrai wants to merge 5 commits into
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added 5 commits
May 5, 2026 20:22
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This PR addresses a few small problems that can cause errors when trying to run
battenberg_wgs.R.--max_allowed_stateto 250 (default used inbattenberg()). This prevents failure when the user does not set the parameter.scanBamHeader()prevents the user from running the script on CRAM files. Default is set to use "chr" prefix.probloci.txt.gzto match what is in the current hg38 Battenberg reference files (https://doi.org/10.48420/30406441).Additionally, a deprecated JVM flag (
UseParallelOldGC) was being used in impute.R that caused the pipeline to fail for newer Java versions (https://bugs.openjdk.org/browse/JDK-8235860). This was corrected.