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Constructor for GATKSamRecord with header only, for unit testing

This commit is contained in:
Mark DePristo 2011-10-19 17:51:48 -04:00
parent 3227143a1c
commit 999a8998ae
1 changed files with 13 additions and 0 deletions
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13
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -36,6 +36,16 @@ public class GATKSamRecord extends BAMRecord {
// These attributes exist in memory only, and are never written to disk. // These attributes exist in memory only, and are never written to disk.
private Map<Object, Object> temporaryAttributes; private Map<Object, Object> temporaryAttributes;
/**
* HACK TO CREATE GATKSAMRECORD WITH ONLY A HEADER FOR TESTING PURPOSES ONLY
* @param header
*/
public GATKSamRecord(final SAMFileHeader header) {
super(header, SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX, SAMRecord.NO_ALIGNMENT_START,
(short)0, (short)255, 0, 1, 0, 1, 0, 0, 0, null);
}
public GATKSamRecord(final SAMFileHeader header, public GATKSamRecord(final SAMFileHeader header,
final int referenceSequenceIndex, final int referenceSequenceIndex,
final int alignmentStart, final int alignmentStart,
@ -57,17 +67,20 @@ public class GATKSamRecord extends BAMRecord {
// *** The following methods are overloaded to cache the appropriate data ***// // *** The following methods are overloaded to cache the appropriate data ***//
/////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////
@Override
public String getReadString() { public String getReadString() {
if ( mReadString == null ) if ( mReadString == null )
mReadString = super.getReadString(); mReadString = super.getReadString();
return mReadString; return mReadString;
} }
@Override
public void setReadString(String s) { public void setReadString(String s) {
super.setReadString(s); super.setReadString(s);
mReadString = s; mReadString = s;
} }
@Override
public SAMReadGroupRecord getReadGroup() { public SAMReadGroupRecord getReadGroup() {
if ( !retrievedReadGroup ) { if ( !retrievedReadGroup ) {
SAMReadGroupRecord tempReadGroup = super.getReadGroup(); SAMReadGroupRecord tempReadGroup = super.getReadGroup();