Steffen Möller pushed to branch upstream at Debian Med / picard-tools
Commits:
03adfbf4 by Steffen Moeller at 2020-11-14T17:49:30+01:00
New upstream version 2.23.8+dfsg
- - - - -
1 changed file:
- src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java
Changes:
=====================================
src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java
=====================================
@@ -140,14 +140,12 @@ public class CollectAlignmentSummaryMetrics extends
SinglePassSamProgram {
IOUtil.assertFileIsWritable(OUTPUT);
if (HISTOGRAM_FILE != null) {
if
(!METRIC_ACCUMULATION_LEVEL.contains(MetricAccumulationLevel.ALL_READS)) {
- log.warn("ReadLength histogram is calculated on all reads
only, but ALL_READS were not " +
- "included in the Metric Accumulation Levels. Adding
ALL_READS so that you get the output you asked for.");
- // This tools is called from "Collect Multiple Metrics" and so
changing the METRIC_ACCUMULATION_LEVEL directly can
- // have unintended consequences....only changing it for this
tool.
- METRIC_ACCUMULATION_LEVEL = new
HashSet<>(METRIC_ACCUMULATION_LEVEL);
-
METRIC_ACCUMULATION_LEVEL.add(MetricAccumulationLevel.ALL_READS);
+ log.error("ReadLength histogram is calculated on all reads
only, but ALL_READS were not " +
+ "included in the Metric Accumulation Levels. Histogram
will not be generated.");
+ HISTOGRAM_FILE=null;
+ } else {
+ IOUtil.assertFileIsWritable(HISTOGRAM_FILE);
}
- IOUtil.assertFileIsWritable(HISTOGRAM_FILE);
}
if (header.getSequenceDictionary().isEmpty()) {
@@ -176,10 +174,12 @@ public class CollectAlignmentSummaryMetrics extends
SinglePassSamProgram {
final
AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
allReadsGroupCollector =
(AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector)
collector.getAllReadsCollector();
- addAllHistogramToMetrics(file, "PAIRED_TOTAL_LENGTH_COUNT",
allReadsGroupCollector.pairCollector);
- addAlignedHistogramToMetrics(file, "PAIRED_ALIGNED_LENGTH_COUNT",
allReadsGroupCollector.pairCollector);
- addAllHistogramToMetrics(file, "UNPAIRED_TOTAL_LENGTH_COUNT",
allReadsGroupCollector.unpairedCollector);
- addAlignedHistogramToMetrics(file, "UNPAIRED_ALIGNED_LENGTH_COUNT",
allReadsGroupCollector.unpairedCollector);
+ if (allReadsGroupCollector != null) {
+ addAllHistogramToMetrics(file, "PAIRED_TOTAL_LENGTH_COUNT",
allReadsGroupCollector.pairCollector);
+ addAlignedHistogramToMetrics(file, "PAIRED_ALIGNED_LENGTH_COUNT",
allReadsGroupCollector.pairCollector);
+ addAllHistogramToMetrics(file, "UNPAIRED_TOTAL_LENGTH_COUNT",
allReadsGroupCollector.unpairedCollector);
+ addAlignedHistogramToMetrics(file,
"UNPAIRED_ALIGNED_LENGTH_COUNT", allReadsGroupCollector.unpairedCollector);
+ }
file.write(OUTPUT);
View it on GitLab:
https://salsa.debian.org/med-team/picard-tools/-/commit/03adfbf4c97adb5d97508cbbbd4e51af9f00d1b3
--
View it on GitLab:
https://salsa.debian.org/med-team/picard-tools/-/commit/03adfbf4c97adb5d97508cbbbd4e51af9f00d1b3
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