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Damnit. Enabling the Picard code to recalculate all of the relevant SAMRecord attribute tags means that I need to have reference bases over all read bases even after realignment (and there are some big indels in dbsnp). Fortunately, I have my trusty IndexedFastaSequenceFile reader handy! Re-enabling the previously broken performance test. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4255 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-09-12 05:06:37 +00:00
parent 87aca64716
commit a0231f073f
2 changed files with 28 additions and 18 deletions
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43
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -430,8 +430,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( reads.size() == 0 ) if ( reads.size() == 0 )
return; return;
final byte[] reference = readsToClean.getReference(referenceReader); byte[] reference = readsToClean.getReference(referenceReader);
final long leftmostIndex = readsToClean.getLocation().getStart(); int leftmostIndex = (int)readsToClean.getLocation().getStart();
final ArrayList<SAMRecord> refReads = new ArrayList<SAMRecord>(); // reads that perfectly match ref final ArrayList<SAMRecord> refReads = new ArrayList<SAMRecord>(); // reads that perfectly match ref
final ArrayList<AlignedRead> altReads = new ArrayList<AlignedRead>(); // reads that don't perfectly match final ArrayList<AlignedRead> altReads = new ArrayList<AlignedRead>(); // reads that don't perfectly match
@ -472,7 +472,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
for ( int j = 0; j < altReads.size(); j++ ) { for ( int j = 0; j < altReads.size(); j++ ) {
AlignedRead toTest = altReads.get(j); AlignedRead toTest = altReads.get(j);
Pair<Integer, Integer> altAlignment = findBestOffset(consensus.str, toTest, (int)leftmostIndex); Pair<Integer, Integer> altAlignment = findBestOffset(consensus.str, toTest, leftmostIndex);
// the mismatch score is the min of its alignment vs. the reference and vs. the alternate // the mismatch score is the min of its alignment vs. the reference and vs. the alternate
int myScore = altAlignment.second; int myScore = altAlignment.second;
@ -520,7 +520,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// start cleaning the appropriate reads // start cleaning the appropriate reads
for ( Pair<Integer, Integer> indexPair : bestConsensus.readIndexes ) { for ( Pair<Integer, Integer> indexPair : bestConsensus.readIndexes ) {
AlignedRead aRead = altReads.get(indexPair.first); AlignedRead aRead = altReads.get(indexPair.first);
if ( !updateRead(bestConsensus.cigar, bestConsensus.positionOnReference, indexPair.second, aRead, (int)leftmostIndex) ) if ( !updateRead(bestConsensus.cigar, bestConsensus.positionOnReference, indexPair.second, aRead, leftmostIndex) )
return; return;
} }
if ( !USE_KNOWN_INDELS_ONLY && !alternateReducesEntropy(altReads, reference, leftmostIndex) ) { if ( !USE_KNOWN_INDELS_ONLY && !alternateReducesEntropy(altReads, reference, leftmostIndex) ) {
@ -588,11 +588,22 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
SAMRecord read = aRead.getRead(); SAMRecord read = aRead.getRead();
read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254)); read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
// fix the attribute tags // before we fix the attribute tags we first need make sure we have enough of the reference sequence
int neededBasesToLeft = Math.max(leftmostIndex - read.getAlignmentStart(), 0);
int neededBasesToRight = Math.max(read.getAlignmentEnd() - leftmostIndex - reference.length + 1, 0);
int neededBases = Math.max(neededBasesToLeft, neededBasesToRight);
if ( neededBases > 0 ) {
int padLeft = Math.max(leftmostIndex-neededBases, 1);
int padRight = Math.min(leftmostIndex+reference.length+neededBases, referenceReader.getSequenceDictionary().getSequence(currentInterval.getContig()).getSequenceLength());
reference = referenceReader.getSubsequenceAt(currentInterval.getContig(), padLeft, padRight).getBases();
leftmostIndex = padLeft;
}
// now, fix the attribute tags
if ( read.getAttribute(SAMTag.NM.name()) != null ) if ( read.getAttribute(SAMTag.NM.name()) != null )
read.setAttribute(SAMTag.NM.name(), SequenceUtil.calculateSamNmTag(read, reference, (int)leftmostIndex-1)); read.setAttribute(SAMTag.NM.name(), SequenceUtil.calculateSamNmTag(read, reference, leftmostIndex-1));
if ( read.getAttribute(SAMTag.UQ.name()) != null ) if ( read.getAttribute(SAMTag.UQ.name()) != null )
read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, reference, (int)leftmostIndex-1)); read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, reference, leftmostIndex-1));
// TODO -- this is only temporary until Tim adds code to recalculate this value // TODO -- this is only temporary until Tim adds code to recalculate this value
if ( read.getAttribute(SAMTag.MD.name()) != null ) if ( read.getAttribute(SAMTag.MD.name()) != null )
read.setAttribute(SAMTag.MD.name(), null); read.setAttribute(SAMTag.MD.name(), null);
@ -613,12 +624,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
} }
} }
private void generateAlternateConsensesFromKnownIndels(final Set<Consensus> altConsensesToPopulate, final long leftmostIndex, final byte[] reference) { private void generateAlternateConsensesFromKnownIndels(final Set<Consensus> altConsensesToPopulate, final int leftmostIndex, final byte[] reference) {
for ( VariantContext knownIndel : knownIndelsToTry.values() ) { for ( VariantContext knownIndel : knownIndelsToTry.values() ) {
if ( knownIndel == null || !knownIndel.isIndel() ) if ( knownIndel == null || !knownIndel.isIndel() )
continue; continue;
byte[] indelStr = knownIndel.isInsertion() ? knownIndel.getAlternateAllele(0).getBases() : Utils.dupBytes((byte)'-', knownIndel.getReference().length()); byte[] indelStr = knownIndel.isInsertion() ? knownIndel.getAlternateAllele(0).getBases() : Utils.dupBytes((byte)'-', knownIndel.getReference().length());
int start = (int)(knownIndel.getStart() - leftmostIndex) + 1; int start = knownIndel.getStart() - leftmostIndex + 1;
Consensus c = createAlternateConsensus(start, reference, indelStr, knownIndel.isDeletion()); Consensus c = createAlternateConsensus(start, reference, indelStr, knownIndel.isDeletion());
if ( c != null ) if ( c != null )
altConsensesToPopulate.add(c); altConsensesToPopulate.add(c);
@ -630,7 +641,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
final ArrayList<AlignedRead> altReadsToPopulate, final ArrayList<AlignedRead> altReadsToPopulate,
final LinkedList<AlignedRead> altAlignmentsToTest, final LinkedList<AlignedRead> altAlignmentsToTest,
final Set<Consensus> altConsenses, final Set<Consensus> altConsenses,
final long leftmostIndex, final int leftmostIndex,
final byte[] reference) { final byte[] reference) {
long totalRawMismatchSum = 0L; long totalRawMismatchSum = 0L;
@ -648,11 +659,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// first, move existing indels (for 1 indel reads only) to leftmost position within identical sequence // first, move existing indels (for 1 indel reads only) to leftmost position within identical sequence
int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read); int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read);
if ( numBlocks == 2 ) { if ( numBlocks == 2 ) {
Cigar newCigar = AlignmentUtils.leftAlignIndel(unclipCigar(read.getCigar()), reference, read.getReadBases(), read.getAlignmentStart()-(int)leftmostIndex, 0); Cigar newCigar = AlignmentUtils.leftAlignIndel(unclipCigar(read.getCigar()), reference, read.getReadBases(), read.getAlignmentStart()-leftmostIndex, 0);
aRead.setCigar(newCigar, false); aRead.setCigar(newCigar, false);
} }
final int startOnRef = read.getAlignmentStart()-(int)leftmostIndex; final int startOnRef = read.getAlignmentStart()-leftmostIndex;
final int rawMismatchScore = mismatchQualitySumIgnoreCigar(aRead, reference, startOnRef, Integer.MAX_VALUE); final int rawMismatchScore = mismatchQualitySumIgnoreCigar(aRead, reference, startOnRef, Integer.MAX_VALUE);
// if this doesn't match perfectly to the reference, let's try to clean it // if this doesn't match perfectly to the reference, let's try to clean it
@ -952,7 +963,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
return true; return true;
} }
private boolean alternateReducesEntropy(final List<AlignedRead> reads, final byte[] reference, final long leftmostIndex) { private boolean alternateReducesEntropy(final List<AlignedRead> reads, final byte[] reference, final int leftmostIndex) {
final int[] originalMismatchBases = new int[reference.length]; final int[] originalMismatchBases = new int[reference.length];
final int[] cleanedMismatchBases = new int[reference.length]; final int[] cleanedMismatchBases = new int[reference.length];
final int[] totalOriginalBases = new int[reference.length]; final int[] totalOriginalBases = new int[reference.length];
@ -967,7 +978,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( read.getRead().getAlignmentBlocks().size() > 1 ) if ( read.getRead().getAlignmentBlocks().size() > 1 )
continue; continue;
int refIdx = read.getOriginalAlignmentStart() - (int)leftmostIndex; int refIdx = read.getOriginalAlignmentStart() - leftmostIndex;
final byte[] readStr = read.getReadBases(); final byte[] readStr = read.getReadBases();
final byte[] quals = read.getBaseQualities(); final byte[] quals = read.getBaseQualities();
@ -983,7 +994,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
} }
// reset and now do the calculation based on the cleaning // reset and now do the calculation based on the cleaning
refIdx = read.getAlignmentStart() - (int)leftmostIndex; refIdx = read.getAlignmentStart() - leftmostIndex;
int altIdx = 0; int altIdx = 0;
Cigar c = read.getCigar(); Cigar c = read.getCigar();
for (int j = 0 ; j < c.numCigarElements() ; j++) { for (int j = 0 ; j < c.numCigarElements() ; j++) {
@ -1031,7 +1042,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( snpsOutput != null ) { if ( snpsOutput != null ) {
if ( didMismatch ) { if ( didMismatch ) {
sb.append(reads.get(0).getRead().getReferenceName() + ":"); sb.append(reads.get(0).getRead().getReferenceName() + ":");
sb.append(((int)leftmostIndex + i)); sb.append((leftmostIndex + i));
if ( stillMismatches ) if ( stillMismatches )
sb.append(" SAME_SNP\n"); sb.append(" SAME_SNP\n");
else else

3
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
View File

@ -37,7 +37,6 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
" -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals", " -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
// executeTest("testIndelRealignerWholeExome", spec2); executeTest("testIndelRealignerWholeExome", spec2);
// TODO: Fix me Eric
} }
} }