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Expose INCLUDE_SECONDARY_ALIGNMENTS for MergeBamAlignment task.
#381
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Codecov Report
@@ Coverage Diff @@
## master #381 +/- ##
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Coverage 91.47% 91.47%
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Files 31 31
Lines 1185 1185
Branches 80 80
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Hits 1084 1084
Misses 101 101 Continue to review full report at Codecov.
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nh13
approved these changes
Jul 29, 2020
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This currently defaults to true, but because of the following bug:
broadinstitute/picard#932
Exposing this flag allows the secondary alignments to not be output and not fail while trying to calculate MD and NM flags.