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GATKSamRecords with efficiency NGSPlatform method

This commit is contained in:
Mark DePristo 2011-10-21 09:38:41 -04:00
parent 94e1898d8f
commit ed74ebcfa1
2 changed files with 34 additions and 5 deletions
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23
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java
View File

@ -1,6 +1,7 @@
package org.broadinstitute.sting.utils.sam; package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.utils.NGSPlatform;
/** /**
* @author ebanks * @author ebanks
@ -15,16 +16,28 @@ public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
// the SAMReadGroupRecord data we're caching // the SAMReadGroupRecord data we're caching
private String mSample = null; private String mSample = null;
private String mPlatform = null; private String mPlatform = null;
private NGSPlatform mNGSPlatform = null;
// because some values can be null, we don't want to duplicate effort // because some values can be null, we don't want to duplicate effort
private boolean retrievedSample = false; private boolean retrievedSample = false;
private boolean retrievedPlatform = false; private boolean retrievedPlatform = false;
private boolean retrievedNGSPlatform = false;
public GATKSAMReadGroupRecord(final String id) {
super(id);
}
public GATKSAMReadGroupRecord(SAMReadGroupRecord record) { public GATKSAMReadGroupRecord(SAMReadGroupRecord record) {
super(record.getReadGroupId(), record); super(record.getReadGroupId(), record);
} }
public GATKSAMReadGroupRecord(SAMReadGroupRecord record, NGSPlatform pl) {
super(record.getReadGroupId(), record);
setPlatform(pl.getDefaultPlatform());
mNGSPlatform = pl;
retrievedPlatform = retrievedNGSPlatform = true;
}
/////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////
// *** The following methods are overloaded to cache the appropriate data ***// // *** The following methods are overloaded to cache the appropriate data ***//
/////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////
@ -55,5 +68,15 @@ public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
super.setPlatform(s); super.setPlatform(s);
mPlatform = s; mPlatform = s;
retrievedPlatform = true; retrievedPlatform = true;
retrievedNGSPlatform = false; // recalculate the NGSPlatform
}
public NGSPlatform getNGSPlatform() {
if ( ! retrievedNGSPlatform ) {
mNGSPlatform = NGSPlatform.fromReadGroupPL(getPlatform());
retrievedNGSPlatform = true;
}
return mNGSPlatform;
} }
} }

16
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -1,6 +1,7 @@
package org.broadinstitute.sting.utils.sam; package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.*; import net.sf.samtools.*;
import org.broadinstitute.sting.utils.NGSPlatform;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map; import java.util.Map;
@ -25,7 +26,7 @@ import java.util.Map;
public class GATKSamRecord extends BAMRecord { public class GATKSamRecord extends BAMRecord {
// the SAMRecord data we're caching // the SAMRecord data we're caching
private String mReadString = null; private String mReadString = null;
private SAMReadGroupRecord mReadGroup = null; private GATKSAMReadGroupRecord mReadGroup = null;
// because some values can be null, we don't want to duplicate effort // because some values can be null, we don't want to duplicate effort
private boolean retrievedReadGroup = false; private boolean retrievedReadGroup = false;
@ -81,17 +82,22 @@ public class GATKSamRecord extends BAMRecord {
} }
@Override @Override
public SAMReadGroupRecord getReadGroup() { public GATKSAMReadGroupRecord getReadGroup() {
if ( !retrievedReadGroup ) { if ( !retrievedReadGroup ) {
SAMReadGroupRecord tempReadGroup = super.getReadGroup(); SAMReadGroupRecord tempReadGroup = super.getReadGroup();
mReadGroup = (tempReadGroup == null ? tempReadGroup : new GATKSAMReadGroupRecord(tempReadGroup)); mReadGroup = (tempReadGroup == null ? null : new GATKSAMReadGroupRecord(tempReadGroup));
retrievedReadGroup = true; retrievedReadGroup = true;
} }
return mReadGroup; return mReadGroup;
} }
public void setReadGroup(SAMReadGroupRecord record) { public NGSPlatform getNGSPlatform() {
mReadGroup = record; return getReadGroup().getNGSPlatform();
}
public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) {
mReadGroup = readGroup;
retrievedReadGroup = true;
} }
/** /**