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Trivial changes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4803 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-12-07 20:06:54 +00:00
parent ca7810f11d
commit 1b6bec8e6b
1 changed files with 45 additions and 27 deletions
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72
java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java
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@ -30,63 +30,81 @@ public class ValidateBAQWalker extends ReadWalker<Integer, Integer> {
@Argument(doc="maximum read length to apply the BAQ calculation too",required=false)
protected int maxReadLen = 1000;
@Argument(doc="",required=false)
protected double bw = 1e-3;
@Argument(doc="only operates on reads with this name",required=false)
protected String readName = null;
@Argument(doc="only prints out detailed information on the impact of BAQ when our implementation differences from the samtools BAQ tag", required=false)
protected boolean onlyPrintOnFailures = false;
@Argument(doc="prints info for each read", required=false)
protected boolean printEachRead = false;
@Argument(doc="Also prints out detailed comparison information when for known calculation differences", required=false)
protected boolean alsoPrintWarnings = false;
@Argument(doc="Include reads without BAQ tag", required=false)
protected boolean includeReadsWithoutBAQTag = false;
int counter = 0;
BAQ baqHMM = new BAQ(1e-3, 0.1, 7, 0); // matches current samtools parameters
BAQ baqHMM = null; // matches current samtools parameters
public void initialize() {
baqHMM = new BAQ(bw, 0.1, 7, 0);
}
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
IndexedFastaSequenceFile refReader = this.getToolkit().getReferenceDataSource().getReference();
if ( (readName == null || readName.equals(read.getReadName())) && read.getReadLength() <= maxReadLen && BAQ.hasBAQTag(read) ) {
byte[] baqFromTag = BAQ.calcBAQFromTag(read, false, false);
if ( (readName == null || readName.equals(read.getReadName())) && read.getReadLength() <= maxReadLen && (includeReadsWithoutBAQTag || BAQ.hasBAQTag(read) ) ) {
byte[] baqFromTag = BAQ.calcBAQFromTag(read, false, includeReadsWithoutBAQTag);
if (counter++ % 1000 == 0) out.printf("Checking read %s (%d)%n", read.getReadName(), counter);
BAQ.BAQCalculationResult baq = baqHMM.calcBAQFromHMM(read, refReader);
boolean fail = false;
boolean print = false;
int badi = 0;
for ( badi = 0; badi < baqFromTag.length; badi++ ) {
if ( baqFromTag[badi] != baq.bq[badi] ) {
if (MathUtils.arrayMin(read.getBaseQualities()) == 0) {
print = true;
out.printf(" different, but Q0 base detected%n");
break;
}
else if (readHasSoftClip(read)) {
print = true;
out.printf(" different, but soft clip detected%n");
break;
} else if (readHasDeletion(read)) {
print = true;
out.printf(" different, but deletion detected%n");
break;
} else {
fail = true; print = true;
break;
if ( BAQ.hasBAQTag(read) ) {
for ( badi = 0; badi < baqFromTag.length; badi++ ) {
if ( baqFromTag[badi] != baq.bq[badi] ) {
if (MathUtils.arrayMin(read.getBaseQualities()) == 0) {
print = true;
out.printf(" different, but Q0 base detected%n");
break;
}
else if (readHasSoftClip(read)) {
print = true;
out.printf(" different, but soft clip detected%n");
break;
} else if (readHasDeletion(read)) {
print = true;
out.printf(" different, but deletion detected%n");
break;
} else {
fail = true; print = true;
break;
}
}
}
}
if ( ! onlyPrintOnFailures || ( print && ( alsoPrintWarnings || fail ) ) ) {
if ( printEachRead || ( print && ( alsoPrintWarnings || fail ) ) ) {
byte[] pos = new byte[baq.bq.length];
for ( int i = 0; i < pos.length; i++ ) pos[i] = (byte)i;
out.printf(" read length : %d%n", read.getReadLength());
out.printf(" read start : %d%n", read.getAlignmentStart());
out.printf(" cigar : %s%n", read.getCigarString());
out.printf(" read bases : %s%n", new String(read.getReadBases()));
out.printf(" ref length : %d%n", baq.refBases.length);
out.printf(" BQ tag : %s%n", read.getStringAttribute(BAQ.BAQ_TAG));
printQuals(" BQ deltas : ", getBAQDeltas(read), true);
if ( BAQ.hasBAQTag(read) ) printQuals(" BQ deltas : ", getBAQDeltas(read), true);
printQuals(" original quals: ", read.getBaseQualities(), true);
printQuals(" baq quals: ", baq.bq, true);
printQuals(" positions : ", pos, true);
printQuals(" original quals: ", read.getBaseQualities());
printQuals(" tag quals: ", baqFromTag);
if ( BAQ.hasBAQTag(read) ) printQuals(" tag quals: ", baqFromTag);
printQuals(" hmm quals: ", baq.bq);
out.printf(" read bases : %s%n", new String(read.getReadBases()));
}
@ -126,7 +144,7 @@ public class ValidateBAQWalker extends ReadWalker<Integer, Integer> {
out.print(prefix);
for ( int i = 0; i < quals.length; i++) {
if ( asInt ) {
out.print((int)quals[i]);
out.printf("%2d", (int)quals[i]);
if ( i+1 != quals.length ) out.print(",");
} else
out.print((char)(quals[i]+33));