Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine.
I note that all integration/unit tests pass except for BaseTransitionTableCalculatorJava, which is already broken. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2182 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks
parent
d5cda76c8b
commit
a184d28ce9
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.iterators;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.Reads;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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/**
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* An iterator which wraps each SAMRecord inside a wrapper class, bringing new functionality to the read while
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@ -18,7 +19,7 @@ public class ReadWrappingIterator implements StingSAMIterator {
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/**
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* Decorate the given iterator inside a ReadWrappingIterator.
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* @param wrappedIterator
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* @param wrappedIterator iterator
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*/
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public ReadWrappingIterator(StingSAMIterator wrappedIterator) {
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this.wrappedIterator = wrappedIterator;
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@ -64,7 +65,7 @@ public class ReadWrappingIterator implements StingSAMIterator {
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* no next exists.
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*/
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public SAMRecord next() {
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return wrappedIterator.next();
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return new GATKSAMRecord(wrappedIterator.next());
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}
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/**
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@ -336,7 +336,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
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for (VCFGenotypeRecord rec : mCurrentRecord.getVCFGenotypeRecords()) {
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if ( rec.isEmptyGenotype() )
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continue;
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;
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double qual = 0;
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if (rec.getAlleles().equals(this.getReference()))
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qual = refQual;
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@ -22,8 +22,6 @@ public class EmpiricalSubstitutionProbabilities extends FourBaseProbabilities {
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UNKNOWN // No idea -- defaulting to 1/3
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}
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private final static String SAM_PLATFORM_TAG = "PL";
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private static TreeMap<String, SequencerPlatform> PLFieldToSequencerPlatform = new TreeMap<String, SequencerPlatform>();
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private static void bind(String s, SequencerPlatform x) {
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PLFieldToSequencerPlatform.put(s, x);
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@ -56,7 +54,7 @@ public class EmpiricalSubstitutionProbabilities extends FourBaseProbabilities {
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if ( lastReadForPL != read ) {
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lastReadForPL = read;
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SAMReadGroupRecord readGroup = read.getReadGroup();
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final String platformName = readGroup == null ? null : (String)readGroup.getAttribute(SAM_PLATFORM_TAG);
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final String platformName = readGroup == null ? null : readGroup.getPlatform();
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plOfLastRead = standardizeSequencerPlatform(platformName);
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}
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@ -0,0 +1,59 @@
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package org.broadinstitute.sting.utils.sam;
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import net.sf.samtools.*;
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/**
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* @author ebanks
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* GATKSAMReadGroupRecord
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*
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* this class extends the samtools SAMReadGroupRecord class and caches important
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* (and oft-accessed) data that's not already cached by the SAMReadGroupRecord class
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*
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*/
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public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
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// the SAMReadGroupRecord data we're caching
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private String mSample = null;
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private String mPlatform = null;
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// because some values can be null, we don't want to duplicate effort
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private boolean retrievedSample = false;
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private boolean retrievedPlatform = false;
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public GATKSAMReadGroupRecord(SAMReadGroupRecord record) {
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super(record.getReadGroupId(), record);
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}
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///////////////////////////////////////////////////////////////////////////////
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// *** The following methods are overloaded to cache the appropriate data ***//
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///////////////////////////////////////////////////////////////////////////////
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public String getSample() {
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if ( !retrievedSample ) {
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mSample = super.getSample();
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retrievedSample = true;
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}
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return mSample;
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}
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public void setSample(String s) {
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super.setSample(s);
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mSample = s;
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retrievedSample = true;
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}
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public String getPlatform() {
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if ( !retrievedPlatform ) {
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mPlatform = super.getPlatform();
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retrievedPlatform = true;
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}
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return mPlatform;
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}
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public void setPlatform(String s) {
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super.setPlatform(s);
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mPlatform = s;
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retrievedPlatform = true;
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}
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}
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@ -0,0 +1,265 @@
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package org.broadinstitute.sting.utils.sam;
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import java.util.List;
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import net.sf.samtools.*;
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/**
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* @author ebanks
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* GATKSAMRecord
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*
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* this class extends the samtools SAMRecord class and caches important
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* (and oft-accessed) data that's not already cached by the SAMRecord class
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*
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* IMPORTANT NOTE: Because ReadGroups are not set through the SAMRecord,
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* if they are ever modified externally then one must also invoke the
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* setReadGroup() method here to ensure that the cache is kept up-to-date.
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*
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*/
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public class GATKSAMRecord extends SAMRecord {
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// the underlying SAMRecord which we are wrapping
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private SAMRecord mRecord;
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// the SAMRecord data we're caching
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private String mReadString = null;
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private SAMReadGroupRecord mReadGroup = null;
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private Boolean mNegativeStrandFlag = null;
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private Boolean mUnmappedFlag = null;
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// because some values can be null, we don't want to duplicate effort
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private boolean retrievedReadGroup = false;
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public GATKSAMRecord(SAMRecord record) {
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super(null); // it doesn't matter - this isn't used
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if ( record == null )
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throw new IllegalArgumentException("The SAMRecord argument cannot be null");
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mRecord = record;
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// because attribute methods are declared to be final (and we can't overload them),
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// we need to actually set all of the attributes here
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// TODO -- remove this exception catch when Picard fixes its internal bug (PIC-291)
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try {
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List<SAMTagAndValue> attributes = record.getAttributes();
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for ( SAMTagAndValue attribute : attributes )
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setAttribute(attribute.tag, attribute.value);
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} catch (NullPointerException picardError) {
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; // do nothing
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}
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}
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///////////////////////////////////////////////////////////////////////////////
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// *** The following methods are overloaded to cache the appropriate data ***//
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///////////////////////////////////////////////////////////////////////////////
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public String getReadString() {
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if ( mReadString == null )
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mReadString = mRecord.getReadString();
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return mReadString;
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}
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public void setReadString(String s) {
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mRecord.setReadString(s);
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mReadString = s;
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}
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public SAMReadGroupRecord getReadGroup() {
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if ( !retrievedReadGroup ) {
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SAMReadGroupRecord tempReadGroup = mRecord.getReadGroup();
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mReadGroup = (tempReadGroup == null ? tempReadGroup : new GATKSAMReadGroupRecord(tempReadGroup));
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retrievedReadGroup = true;
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}
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return mReadGroup;
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}
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public void setReadGroup(SAMReadGroupRecord record) {
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mReadGroup = record;
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}
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public boolean getReadUnmappedFlag() {
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if ( mUnmappedFlag == null )
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mUnmappedFlag = mRecord.getReadUnmappedFlag();
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return mUnmappedFlag;
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}
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public void setReadUmappedFlag(boolean b) {
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mRecord.setReadUmappedFlag(b);
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mUnmappedFlag = b;
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}
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public boolean getReadNegativeStrandFlag() {
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if ( mNegativeStrandFlag == null )
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mNegativeStrandFlag = mRecord.getReadNegativeStrandFlag();
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return mNegativeStrandFlag;
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}
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public void setReadNegativeStrandFlag(boolean b) {
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mRecord.setReadNegativeStrandFlag(b);
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mNegativeStrandFlag = b;
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}
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/////////////////////////////////////////////////////////////////////
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// *** The following methods are final and cannot be overridden ***//
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/////////////////////////////////////////////////////////////////////
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//public final Object getAttribute(String s) { return mRecord.getAttribute(s); }
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//public final Integer getIntegerAttribute(java.lang.String s) { return mRecord.getIntegerAttribute(s); }
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//public final Short getShortAttribute(String s) { return mRecord.getShortAttribute(s); }
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//public final Byte getByteAttribute(java.lang.String s) { return mRecord.getByteAttribute(s); }
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//public final void setAttribute(String s, Object o) { mRecord.setAttribute(s, o); }
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//public final List<net.sf.samtools.SAMRecord.SAMTagAndValue> getAttributes() { return mRecord.getAttributes(); }
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/////////////////////////////////////////////////////////////////////////////////
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// *** The following methods just call the appropriate method in the record ***//
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/////////////////////////////////////////////////////////////////////////////////
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public String getReadName() { return mRecord.getReadName(); }
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public int getReadNameLength() { return mRecord.getReadNameLength(); }
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public void setReadName(String s) { mRecord.setReadName(s); }
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public byte[] getReadBases() { return mRecord.getReadBases(); }
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public void setReadBases(byte[] bytes) { mRecord.setReadBases(bytes); }
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public int getReadLength() { return mRecord.getReadLength(); }
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public String getBaseQualityString() { return mRecord.getBaseQualityString(); }
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public void setBaseQualityString(java.lang.String s) { mRecord.setBaseQualityString(s); }
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public byte[] getBaseQualities() { return mRecord.getBaseQualities(); }
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public void setBaseQualities(byte[] bytes) { mRecord.setBaseQualities(bytes); }
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public byte[] getOriginalBaseQualities() { return mRecord.getOriginalBaseQualities(); }
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public void setOriginalBaseQualities(byte[] bytes) { mRecord.setOriginalBaseQualities(bytes); }
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public String getReferenceName() { return mRecord.getReferenceName(); }
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public void setReferenceName(String s) { mRecord.setReferenceName(s); }
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public Integer getReferenceIndex() { return mRecord.getReferenceIndex(); }
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public void setReferenceIndex(int i) { mRecord.setReferenceIndex(i); }
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public String getMateReferenceName() { return mRecord.getMateReferenceName(); }
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public void setMateReferenceName(String s) { mRecord.setMateReferenceName(s); }
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public Integer getMateReferenceIndex() { return mRecord.getMateReferenceIndex(); }
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public void setMateReferenceIndex(int i) { mRecord.setMateReferenceIndex(i); }
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public int getAlignmentStart() { return mRecord.getAlignmentStart(); }
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public void setAlignmentStart(int i) { mRecord.setAlignmentStart(i); }
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public int getAlignmentEnd() { return mRecord.getAlignmentEnd(); }
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public int getUnclippedStart() { return mRecord.getUnclippedStart(); }
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public int getUnclippedEnd() { return mRecord.getUnclippedEnd(); }
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public void setAlignmentEnd(int i) { mRecord.setAlignmentEnd(i); }
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public int getMateAlignmentStart() { return mRecord.getMateAlignmentStart(); }
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public void setMateAlignmentStart(int i) { mRecord.setMateAlignmentStart(i); }
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public int getInferredInsertSize() { return mRecord.getInferredInsertSize(); }
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public void setInferredInsertSize(int i) { mRecord.setInferredInsertSize(i); }
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public int getMappingQuality() { return mRecord.getMappingQuality(); }
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public void setMappingQuality(int i) { mRecord.setMappingQuality(i); }
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public String getCigarString() { return mRecord.getCigarString(); }
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public void setCigarString(String s) { mRecord.setCigarString(s); }
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public Cigar getCigar() { return mRecord.getCigar(); }
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public int getCigarLength() { return mRecord.getCigarLength(); }
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public void setCigar(Cigar cigar) { mRecord.setCigar(cigar); }
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public int getFlags() { return mRecord.getFlags(); }
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public void setFlags(int i) { mRecord.setFlags(i); }
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public boolean getReadPairedFlag() { return mRecord.getReadPairedFlag(); }
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public boolean getProperPairFlag() { return mRecord.getProperPairFlag(); }
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public boolean getMateUnmappedFlag() { return mRecord.getMateUnmappedFlag(); }
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public boolean getMateNegativeStrandFlag() { return mRecord.getMateNegativeStrandFlag(); }
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public boolean getFirstOfPairFlag() { return mRecord.getFirstOfPairFlag(); }
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public boolean getSecondOfPairFlag() { return mRecord.getSecondOfPairFlag(); }
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public boolean getNotPrimaryAlignmentFlag() { return mRecord.getNotPrimaryAlignmentFlag(); }
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public boolean getReadFailsVendorQualityCheckFlag() { return mRecord.getReadFailsVendorQualityCheckFlag(); }
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public boolean getDuplicateReadFlag() { return mRecord.getDuplicateReadFlag(); }
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public void setReadPairedFlag(boolean b) { mRecord.setReadPairedFlag(b); }
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public void setProperPairFlag(boolean b) { mRecord.setProperPairFlag(b); }
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public void setMateUnmappedFlag(boolean b) { mRecord.setMateUnmappedFlag(b); }
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public void setMateNegativeStrandFlag(boolean b) { mRecord.setMateNegativeStrandFlag(b); }
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public void setFirstOfPairFlag(boolean b) { mRecord.setFirstOfPairFlag(b); }
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public void setSecondOfPairFlag(boolean b) { mRecord.setSecondOfPairFlag(b); }
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public void setNotPrimaryAlignmentFlag(boolean b) { mRecord.setNotPrimaryAlignmentFlag(b); }
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public void setReadFailsVendorQualityCheckFlag(boolean b) { mRecord.setReadFailsVendorQualityCheckFlag(b); }
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public void setDuplicateReadFlag(boolean b) { mRecord.setDuplicateReadFlag(b); }
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public net.sf.samtools.SAMFileReader.ValidationStringency getValidationStringency() { return mRecord.getValidationStringency(); }
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public void setValidationStringency(net.sf.samtools.SAMFileReader.ValidationStringency validationStringency) { mRecord.setValidationStringency(validationStringency); }
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public SAMFileHeader getHeader() { return mRecord.getHeader(); }
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public void setHeader(SAMFileHeader samFileHeader) { mRecord.setHeader(samFileHeader); }
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public byte[] getVariableBinaryRepresentation() { return mRecord.getVariableBinaryRepresentation(); }
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public int getAttributesBinarySize() { return mRecord.getAttributesBinarySize(); }
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public String format() { return mRecord.format(); }
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public List<AlignmentBlock> getAlignmentBlocks() { return mRecord.getAlignmentBlocks(); }
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public List<SAMValidationError> validateCigar(long l) { return mRecord.validateCigar(l); }
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public boolean equals(Object o) { return mRecord.equals(o); }
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public int hashCode() { return mRecord.hashCode(); }
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public List<SAMValidationError> isValid() { return mRecord.isValid(); }
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public Object clone() throws CloneNotSupportedException { return mRecord.clone(); }
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public String toString() { return mRecord.toString(); }
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}
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