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broadinstitute / picard Public

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Fix crash on PF_READS == 0 for AlignmentSummaryMetricsCollector#1871

Merged

kockan merged 6 commits intomasterbroadinstitute/picard:masterfrom can_no_pf_reads_fixbroadinstitute/picard:can_no_pf_reads_fixCopy head branch name to clipboard

May 10, 2023

+45-1

Conversation Commits6 (6)Checks Files changed

Commits

Commits on Apr 13, 2023

Create a (mostly) empty metrics file instead of giving a stacktrace if no reads pass Illumina filters.
kockan
committed

Commits on Apr 14, 2023

Added test for the PF_READS == 0 case. The new check should make checking if TOTAL_READS > 0 redundant, so that's removed now.
kockan
committed
Added the test file
kockan
committed

Commits on May 9, 2023

Use a PicardException with an informative message instead.
kockan
committed
Reverting latest changes to check why some tests fail.
kockan
committed
Add another check to make sure TOTAL_READS > 0 before throwing a PicardException for PF_READS == 0
kockan
committed

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