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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
Merged

Fix crash on PF_READS == 0 for AlignmentSummaryMetricsCollector #1871

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0629d95
Create a (mostly) empty metrics file instead of giving a stacktrace i…
kockan Apr 13, 2023
b24e512
Added test for the PF_READS == 0 case. The new check should make chec…
kockan Apr 14, 2023
3e72e7b
Added the test file
kockan Apr 14, 2023
933a605
Use a PicardException with an informative message instead.
kockan May 9, 2023
b80aa0c
Reverting latest changes to check why some tests fail.
kockan May 9, 2023
4b92bbc
Add another check to make sure TOTAL_READS > 0 before throwing a Pica…
kockan May 9, 2023
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2 changes: 1 addition & 1 deletion src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
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Original file line number Diff line number Diff line change
Expand Up @@ -261,7 +261,7 @@ public void acceptRecord(final SAMRecordAndReference samRecordAndReference) {
@Override
public void finish() {
//summarize read data
if (metrics.TOTAL_READS > 0) {
if (metrics.TOTAL_READS > 0 && metrics.PF_READS > 0) {
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metrics.PCT_PF_READS = (double) metrics.PF_READS / (double) metrics.TOTAL_READS;
metrics.PCT_ADAPTER = adapterReads / (double) metrics.PF_READS;
metrics.MEAN_READ_LENGTH = readLengthHistogram.getMean();
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