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Updated Picard with fix for Doug Voet. Thanks Alec. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2015 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-11-11 02:01:08 +00:00
parent 2e4782f202
commit bae4d3f7ea
10 changed files with 9 additions and 9 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -384,7 +384,7 @@ public class GenomeAnalysisEngine {
rg_sets.add(groups);
for (SAMReadGroupRecord g : r.getFileHeader().getReadGroups()) {
if (hm.hasGroupIdDuplicates()) { // Check if there were read group clashes with hasGroupIdDuplicates and if so:
if (hm.hasReadGroupCollisions()) { // Check if there were read group clashes with hasGroupIdCollisions and if so:
// use HeaderMerger to translate original read group id from the reader into the read group id in the
// merged stream, and save that remapped read group id to associate it with specific reader
groups.add(hm.getReadGroupId(r, g.getReadGroupId()));

2
java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
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@ -235,7 +235,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
final SAMRecord record = iterator.next();
addIfNotEmpty(iterator);
if (this.samHeaderMerger.hasGroupIdDuplicates()) {
if (this.samHeaderMerger.hasReadGroupCollisions()) {
final String id = (String) record.getAttribute(ReservedTagConstants.READ_GROUP_ID);
final String newId = this.samHeaderMerger.getReadGroupId(iterator.getReader(), id);
record.setAttribute(ReservedTagConstants.READ_GROUP_ID, newId);

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settings/repository/edu.mit.broad/picard-private-1084.jar → settings/repository/edu.mit.broad/picard-private-1105.jar
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settings/repository/edu.mit.broad/picard-private-1084.xml → settings/repository/edu.mit.broad/picard-private-1105.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard-private" revision="1084" status="integration" publication="20091016142400" />
<info organisation="edu.mit.broad" module="picard-private" revision="1105" status="integration" publication="20091110205100" />
</ivy-module>

3
settings/repository/net.sf/picard-1.05.140.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.05.140" status="release" />
</ivy-module>

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settings/repository/net.sf/picard-1.05.140.jar → settings/repository/net.sf/picard-1.07.165.jar
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settings/repository/net.sf/picard-1.07.165.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.07.165" status="release" />
</ivy-module>

3
settings/repository/net.sf/sam-1.05.140.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.05.140" status="release" />
</ivy-module>

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settings/repository/net.sf/sam-1.05.140.jar → settings/repository/net.sf/sam-1.07.165.jar
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3
settings/repository/net.sf/sam-1.07.165.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.07.165" status="release" />
</ivy-module>