update picard 2.18.11 -> 2.20.3 #977
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…wed by picard commas, single quotes, etc.
compare only reads in sam post-depletion, allowing us to ignore header differences due to varying versions of picard/samtools/htslib; remove related permutations of expected output from tests
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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? |
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Here's the (human-data-centric) discussion upstream about the breaking changes to htsjdk: |
add new test assertion, "assertEqualSamHeaders" to address this inline ToDo for TestFastqBam(): "Note for developers: if you're fixing the tests to handle non-bugs (ie our testing here is too brittle), let's just replace a lot of this in the future with code that just reads the header, sorts it, and tests for equality of sorted values in the RG line (and stricter equality in the non-header lines). This is kind of hacky."
add debug statements to install-viral-ngs.sh Docker script
required by GATK 3.8 conda package
….file to sanitize fasta file IDs fasta ID is sanitized for picard CreateSequenceDictionary to adhere to character set restrictions in SAM/BAM RNAME spec. see: samtools/hts-specs#333 Roll back test input now that we are doing the sanitization. As of this commit, sanitization is only performed on fasta files destined for CreateSequenceDictionary
change lz4 dependency from lz4-bin from bioconda to lz4-c from conda-forge, v131->v1.9.1
switch to picard-slim package (sans 'r'); specify USE_JDK_DEFLATER=true and USE_JDK_INFLATER=true until bug in Intel deflator is fixed to prevent sporadic crashes
revert to corrected test input
dpark01
approved these changes
Sep 11, 2019
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This PR does the following:
picard2.18.11 -> 2.20.3