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Fix crash on PF_READS == 0 for AlignmentSummaryMetricsCollector #1871

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merged 6 commits into from May 10, 2023

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kockan
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@kockan kockan commented Apr 13, 2023

Description


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

Related to the following issue: #1862

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@kockan kockan requested review from droazen and kachulis April 13, 2023 15:09
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Thanks @kockan this looks reasonable. Could you just add a test demonstrating the fix?

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@kachulis kachulis left a comment

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This looks good to me, thanks @kockan!

@kockan kockan merged commit 78892bf into master May 10, 2023
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@kockan kockan deleted the can_no_pf_reads_fix branch May 10, 2023 14:45
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Successfully merging this pull request may close these issues.

CollectAlignmentSummaryMetrics fails on some small inputs due to unsafe Histogram methods
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