Update htsjdk to 4.0.2 #340
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update htsjdk and picard to latest and greatest, some style changes for qbamfilter, along with a test to create a CRAM and run through the filter
delocalizer
approved these changes
Nov 29, 2023
htsjdk now has a more standard approach to naming BAM and CRAM indexes, and so the renameIndex method that is used by FileMerger needed an overhaul
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Description
Update to the latest (4.0.2) version of
htsjdk.A few tweaks (as prescribed by my IDE) to
qbamfilter.Addition of test in
qbamfilterthat creates CRAM and checks MD tagType of change
Library update
How Has This Been Tested?
Unit tests pass
Are WDL Updates Required?
No
Checklist: