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broadinstitute / viral-ngs

Viral genomics analysis pipelines
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update picard 2.18.11 -> 2.20.3 #977

Closed tomkinsc closed 4 years ago

tomkinsc commented 4 years ago

This PR does the following:

dpark01 commented 4 years ago

Wait, regarding this commit, maybe instead of "fixing" the test input file, should we be adding code that sanitizes input all the time now? Because apparently this wasn't an issue for old versions of Picard, but now it is, so these changes will break things that used to work?

tomkinsc commented 4 years ago

Here's the (human-data-centric) discussion upstream about the breaking changes to htsjdk: https://github.com/samtools/hts-specs/pull/333 Allowing certain characters in the reference name seems put resulting files out of spec with the SAM standard. We can sanitize if you think that's best. Or maybe if the reference sequences we include are from GenBank including the accession in addition to the sequence name would resolve the issue and be more 'correct.'