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Preserve RG information on new GATKSAMRecord from SAMRecord

This commit is contained in:
Mauricio Carneiro 2011-11-09 12:46:27 -05:00
parent f9530e0768
commit f080f64f99
1 changed files with 43 additions and 21 deletions
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64
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -87,7 +87,12 @@ public class GATKSAMRecord extends BAMRecord {
read.getMateAlignmentStart(), read.getMateAlignmentStart(),
read.getInferredInsertSize(), read.getInferredInsertSize(),
null); null);
super.clearAttributes(); SAMReadGroupRecord samRG = read.getReadGroup();
clearAttributes();
if (samRG != null) {
GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
setReadGroup(rg);
}
} }
public GATKSAMRecord(final SAMFileHeader header, public GATKSAMRecord(final SAMFileHeader header,
@ -134,6 +139,21 @@ public class GATKSAMRecord extends BAMRecord {
return mReadGroup; return mReadGroup;
} }
@Override
public int hashCode() {
return super.hashCode();
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (!(o instanceof GATKSAMRecord)) return false;
// note that we do not consider the GATKSAMRecord internal state at all
return super.equals(o);
}
/** /**
* Efficient caching accessor that returns the GATK NGSPlatform of this read * Efficient caching accessor that returns the GATK NGSPlatform of this read
* @return * @return
@ -147,11 +167,9 @@ public class GATKSAMRecord extends BAMRecord {
retrievedReadGroup = true; retrievedReadGroup = true;
} }
// ///////////////////////////////////////////////////////////////////////////////
// // *** ReduceReads functions ***//
// Reduced read functions ///////////////////////////////////////////////////////////////////////////////
//
//
public byte[] getReducedReadCounts() { public byte[] getReducedReadCounts() {
if ( ! retrievedReduceReadCounts ) { if ( ! retrievedReduceReadCounts ) {
@ -170,6 +188,12 @@ public class GATKSAMRecord extends BAMRecord {
return getReducedReadCounts()[i]; return getReducedReadCounts()[i];
} }
///////////////////////////////////////////////////////////////////////////////
// *** GATKSAMRecord specific methods ***//
///////////////////////////////////////////////////////////////////////////////
/** /**
* Checks whether an attribute has been set for the given key. * Checks whether an attribute has been set for the given key.
* *
@ -223,28 +247,26 @@ public class GATKSAMRecord extends BAMRecord {
return null; return null;
} }
@Override /**
public int hashCode() { * Checks whether if the read has any bases.
return super.hashCode(); *
} * Empty reads can be dangerous as it may have no cigar strings, no read names and
* other missing attributes.
@Override *
public boolean equals(Object o) { * @return true if the read has no bases
if (this == o) return true; */
if (!(o instanceof GATKSAMRecord)) return false;
// note that we do not consider the GATKSAMRecord internal state at all
return super.equals(o);
}
public boolean isEmpty() { public boolean isEmpty() {
return this.getReadLength() == 0; return this.getReadLength() == 0;
} }
/**
* Clears all attributes except ReadGroup of the read.
*/
public void simplify () { public void simplify () {
GATKSAMReadGroupRecord rg = getReadGroup(); GATKSAMReadGroupRecord rg = getReadGroup();
this.clearAttributes(); this.clearAttributes();
setReadGroup(rg); setReadGroup(rg);
} }
} }