[med-svn] [Git][med-team/picard-tools][master] 4 commits: routine-update: New upstream version
Steffen Möller
gitlab at salsa.debian.org
Sat Nov 14 19:09:41 GMT 2020
Steffen Möller pushed to branch master at Debian Med / picard-tools
Commits:
5d74ec74 by Steffen Moeller at 2020-11-14T17:49:25+01:00
routine-update: New upstream version
- - - - -
03adfbf4 by Steffen Moeller at 2020-11-14T17:49:30+01:00
New upstream version 2.23.8+dfsg
- - - - -
cc63008e by Steffen Moeller at 2020-11-14T17:50:29+01:00
Update upstream source from tag 'upstream/2.23.8+dfsg'
Update to upstream version '2.23.8+dfsg'
with Debian dir 15bbbd4f58215a3142093009412a19664f33865f
- - - - -
3e57ca3a by Steffen Moeller at 2020-11-14T20:09:13+01:00
Established compatibility with bcbio
- - - - -
5 changed files:
- debian/bin/PicardCommandLine
- debian/changelog
- debian/picard-tools.links
- debian/upstream/metadata
- src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java
Changes:
=====================================
debian/bin/PicardCommandLine
=====================================
@@ -1,17 +1,42 @@
#!/bin/sh
set -eu
PRG="$(basename -- "$0")"
+
+JavOpt=""
+PicardProg=""
+PicardOpts=""
+
+for i in $@
+do
+ if [ ! -n "$PicardProg" ]; then
+ if echo $i|egrep "^-X"; then
+ JavOpt="$JavOpt $i"
+ else
+ PicardProg="$i"
+ fi
+ else
+ PicardOpts="$PicardOpts $i"
+ fi
+done
+echo JavOpt: $JavOpt
+echo PicardProg: $PicardProg
+echo PicardOpts: $PicardOpts
+
case "$PRG" in
+picard)
+ echo 1>&2 'Warning: picard is not official and should be replaced by PicardCommandLine, only accepting this temporarily to help development of bcbio package.'
+ ;;
picard-tools)
echo 1>&2 'Warning: picard-tools is deprecated and should be replaced by PicardCommandLine'
;;
PicardCommandLine)
;;
*)
- set -- "$PRG" "$@"
+ PicardProg=$PRG
+ PicardsOpts="$PicardProg $PicardOpts"
;;
esac
export USE_LIBRARY_PATH=USE_LIBRARY_PATH
export PICARD_CLASSPATH=/usr/share/java/picard.jar:/usr/share/java/htsjdk.jar:/usr/share/java/guava.jar:/usr/lib/jvm/default-java/lib/tools.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/gkl.jar:/usr/share/java/gatk-native-bindings.jar:/usr/share/java/barclay.jar
-exec java ${JAVA_OPTIONS-} -cp $PICARD_CLASSPATH picard.cmdline.PicardCommandLine "$@"
+exec java ${JAVA_OPTIONS-} $JavOpt -cp $PICARD_CLASSPATH picard.cmdline.PicardCommandLine $PicardProg $PicardOpts
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+picard-tools (2.23.8+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * Added link from /usr/lib/debian-med/bin/picard to PicardCommandLine
+ only temporarily for now for presumed compatibility with what conda
+ is offering and what bcbio is apparently expecting.
+ * Added reference to d/u/metadata as suggested by upstream.
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 14 Nov 2020 17:50:50 +0100
+
picard-tools (2.23.7+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/picard-tools.links
=====================================
@@ -1,2 +1,4 @@
usr/bin/PicardCommandLine usr/bin/picard-tools
usr/share/man/man1/PicardCommandLine.1 usr/share/man/man1/picard-tools.1
+# Temporarily to help bcbio
+usr/bin/PicardCommandLine usr/share/debian-med/bin/picard
=====================================
debian/upstream/metadata
=====================================
@@ -1,13 +1,19 @@
Bug-Database: https://github.com/broadinstitute/picard/issues
Bug-Submit: https://github.com/broadinstitute/picard/issues/new
+Reference:
+ - Auhtor: Broad Institute
+ Title: Picard toolkit
+ Year: 2019
+ Journal: Broad Institute, GitHub repository
+ URL: http://broadinstitute.github.io/picard/
Registry:
- - Name: OMICtools
- Entry: OMICS_01066
- - Name: bio.tools
- Entry: Picard_tools
- - Name: SciCrunch
- Entry: SCR_006525
- - Name: conda:bioconda
- Entry: picard
+ - Name: OMICtools
+ Entry: OMICS_01066
+ - Name: bio.tools
+ Entry: Picard_tools
+ - Name: SciCrunch
+ Entry: SCR_006525
+ - Name: conda:bioconda
+ Entry: picard
Repository: https://github.com/broadinstitute/picard.git
Repository-Browse: https://github.com/broadinstitute/picard
=====================================
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/-/compare/8c40b22da8e48ea29a4f53ae6226bac949147103...3e57ca3ad66965f08a0845cb2dadf8c93db5d8b8
--
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/8c40b22da8e48ea29a4f53ae6226bac949147103...3e57ca3ad66965f08a0845cb2dadf8c93db5d8b8
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