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Fix crash on PF_READS == 0 for AlignmentSummaryMetricsCollector #1871

Merged
merged 6 commits into from
May 10, 2023
Merged

Fix crash on PF_READS == 0 for AlignmentSummaryMetricsCollector #1871

merged 6 commits into from
May 10, 2023

Commits on Apr 13, 2023

  1. Create a (mostly) empty metrics file instead of giving a stacktrace i… 

    …f no reads pass Illumina filters.
    @kockan
    kockan committed Apr 13, 2023
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Commits on Apr 14, 2023

  1. Added test for the PF_READS == 0 case. The new check should make chec… 

    …king if TOTAL_READS > 0 redundant, so that's removed now.
    @kockan
    kockan committed Apr 14, 2023
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  2. Added the test file

    @kockan
    kockan committed Apr 14, 2023
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Commits on May 9, 2023

  1. Use a PicardException with an informative message instead.

    @kockan
    kockan committed May 9, 2023
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  2. Reverting latest changes to check why some tests fail.

    @kockan
    kockan committed May 9, 2023
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  3. Add another check to make sure TOTAL_READS > 0 before throwing a Pica… 

    …rdException for PF_READS == 0
    @kockan
    kockan committed May 9, 2023
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