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PicardTask to use the Intel inflater/deflater only if it is safe, by default #368
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Codecov Report
@@ Coverage Diff @@
## master #368 +/- ##
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+ Coverage 91.55% 91.56% +0.01%
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Files 31 31
Lines 1184 1186 +2
Branches 81 81
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+ Hits 1084 1086 +2
Misses 100 100
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nh13
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Oct 8, 2019
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@clintval this should be unblocked given fulcrumgenomics/commons#59 is merged. |
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@nh13 all set. Is TravisCI no longer enabled in this repository? |
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Re-opening to see if I can get travis-ci to build. |
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@clintval looks like it wasn't triggering, re-opening did the trick |
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Many of my Dagr pipelines now require the Intel Inflater/Deflater to be conditionally turned off across all executables that use htsjdk because of IntelLabs/GKL#101. Can we intelligently use the Intel Inflater/Deflater, or not, on any Picard task as a default?
Followup to: #367 (including your comment) and fulcrumgenomics/fgbio#534
Note: None of my recent PRs provide parameterization, or default-setting, for GATK tasks!
I have tested this using pipelines that have Picard tasks and confirm it works as expected!