diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 227a652a0..aef85d491 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -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())); diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java index a70ebcc5d..265df5879 100644 --- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java +++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java @@ -235,22 +235,15 @@ public class MergingSamRecordIterator2 implements CloseableIterator, 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 diff --git a/settings/repository/edu.mit.broad/picard-private-1105.jar b/settings/repository/edu.mit.broad/picard-private-1084.jar similarity index 81% rename from settings/repository/edu.mit.broad/picard-private-1105.jar rename to settings/repository/edu.mit.broad/picard-private-1084.jar index e4f49d57e..66dce1a99 100644 Binary files a/settings/repository/edu.mit.broad/picard-private-1105.jar and b/settings/repository/edu.mit.broad/picard-private-1084.jar differ diff --git a/settings/repository/edu.mit.broad/picard-private-1105.xml b/settings/repository/edu.mit.broad/picard-private-1084.xml similarity index 63% rename from settings/repository/edu.mit.broad/picard-private-1105.xml rename to settings/repository/edu.mit.broad/picard-private-1084.xml index aeaf508ca..18204e9a7 100644 --- a/settings/repository/edu.mit.broad/picard-private-1105.xml +++ b/settings/repository/edu.mit.broad/picard-private-1084.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/picard-1.07.165.jar b/settings/repository/net.sf/picard-1.05.140.jar similarity index 66% rename from settings/repository/net.sf/picard-1.07.165.jar rename to settings/repository/net.sf/picard-1.05.140.jar index aa93c00b1..b93c47700 100644 Binary files a/settings/repository/net.sf/picard-1.07.165.jar and b/settings/repository/net.sf/picard-1.05.140.jar differ diff --git a/settings/repository/net.sf/picard-1.05.140.xml b/settings/repository/net.sf/picard-1.05.140.xml new file mode 100644 index 000000000..aac545236 --- /dev/null +++ b/settings/repository/net.sf/picard-1.05.140.xml @@ -0,0 +1,3 @@ + + + diff --git a/settings/repository/net.sf/picard-1.07.165.xml b/settings/repository/net.sf/picard-1.07.165.xml deleted file mode 100644 index 33f651303..000000000 --- a/settings/repository/net.sf/picard-1.07.165.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/net.sf/sam-1.07.165.jar b/settings/repository/net.sf/sam-1.05.140.jar similarity index 82% rename from settings/repository/net.sf/sam-1.07.165.jar rename to settings/repository/net.sf/sam-1.05.140.jar index cc710b855..e983077fd 100644 Binary files a/settings/repository/net.sf/sam-1.07.165.jar and b/settings/repository/net.sf/sam-1.05.140.jar differ diff --git a/settings/repository/net.sf/sam-1.05.140.xml b/settings/repository/net.sf/sam-1.05.140.xml new file mode 100644 index 000000000..a9e5a57b2 --- /dev/null +++ b/settings/repository/net.sf/sam-1.05.140.xml @@ -0,0 +1,3 @@ + + + diff --git a/settings/repository/net.sf/sam-1.07.165.xml b/settings/repository/net.sf/sam-1.07.165.xml deleted file mode 100644 index 1fd90c4f9..000000000 --- a/settings/repository/net.sf/sam-1.07.165.xml +++ /dev/null @@ -1,3 +0,0 @@ - - -