Draft: Fix memory problem with alt hla #87
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…n ALT processing. Removed FLAG_RUN_SLIM_WORKFLOW that is unusable for years. Renamed FLAG_USE_EXISTING_PAIRED_BAMS to FLAG_USE_ONLY_EXISTING_PAIRED_BAMS
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Sorry, the COWorkflowsBasePlugin 1.4.2 bump has to be rolled back. I somehow get compilation problems now, and have no clue why, because the original changes are actually really old. |
vinjana
changed the title
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Looks like a lot, but most changes are only refactorings (mostly groovification, layout, and some other small things).
bwaPostAltJsK8Optionsto allow setting opt K8 options forbwa-postalt.jsSAMPESORT_MEMSIZEto allow reducing memory for SAM sorting. Default: ~2 GiB.FLAG_USE_EXISTING_PAIRED_BAMSwas renamed toFLAG_USE_ONLY_EXISTING_PAIRED_BAMSFLAG_RUN_SLIM_WORKFLOW. Corresponding code is unused for years.