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New Picard is breaking one of the integration tests. 

Revert until we find out whether the cause is legit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2017 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-11-11 03:59:32 +00:00
parent 499e7d1d75
commit 8406325247
10 changed files with 16 additions and 23 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

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.hasReadGroupCollisions()) { // Check if there were read group clashes with hasGroupIdCollisions and if so:
if (hm.hasGroupIdDuplicates()) { // Check if there were read group clashes with hasGroupIdDuplicates 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()));

23
java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
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@ -235,22 +235,15 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
final SAMRecord record = iterator.next();
addIfNotEmpty(iterator);
// Fix the read group if needs be
if (this.samHeaderMerger.hasReadGroupCollisions()) {
final String oldGroupId = (String) record.getAttribute(ReservedTagConstants.READ_GROUP_ID);
if (oldGroupId != null ) {
final String newGroupId = this.samHeaderMerger.getReadGroupId(iterator.getReader(), oldGroupId);
record.setAttribute(ReservedTagConstants.READ_GROUP_ID, newGroupId);
}
if (this.samHeaderMerger.hasGroupIdDuplicates()) {
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);
}
// Fix the program group if needs be
if (this.samHeaderMerger.hasProgramGroupCollisions()) {
final String oldGroupId = (String) record.getAttribute(ReservedTagConstants.PROGRAM_GROUP_ID);
if (oldGroupId != null ) {
final String newGroupId = this.samHeaderMerger.getProgramGroupId(iterator.getReader(), oldGroupId);
record.setAttribute(ReservedTagConstants.PROGRAM_GROUP_ID, newGroupId);
}
final String oldProgramGroupId = (String) record.getAttribute(SAMTag.PG.toString());
if (oldProgramGroupId != null) {
final String newProgramGroupId = this.samHeaderMerger.getProgramGroupId(iterator.getReader(), oldProgramGroupId);
record.setAttribute(SAMTag.PG.toString(), newProgramGroupId);
}
// if we don't have a read group, set one correctly

BIN
settings/repository/edu.mit.broad/picard-private-1105.jar → settings/repository/edu.mit.broad/picard-private-1084.jar
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2
settings/repository/edu.mit.broad/picard-private-1105.xml → settings/repository/edu.mit.broad/picard-private-1084.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard-private" revision="1105" status="integration" publication="20091110205100" />
<info organisation="edu.mit.broad" module="picard-private" revision="1084" status="integration" publication="20091016142400" />
</ivy-module>

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

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

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

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