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LocusIterationByState is now the system deafult. Fixed Aaron's build problem 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1552 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-09-09 01:28:05 +00:00
parent ea6ffd3796
commit ec0f6f23c7
7 changed files with 35 additions and 124 deletions
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6
java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java
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@ -135,8 +135,8 @@ public class GATKArgumentCollection {
public int numberOfThreads = 1; public int numberOfThreads = 1;
@Element(required = false) @Element(required = false)
@Argument(fullName = "LocusIteratorByState", shortName = "LIBS", doc = "Should we use the new LocusIteratorByState or the old LocusIteratorByHanger?", required = false) @Argument(fullName = "LocusIteratorByHanger", shortName = "LIBH", doc = "Should we use the new LocusIteratorByState or the old LocusIteratorByHanger?", required = false)
public Boolean useLocusIteratorByState = false; public Boolean useLocusIteratorByHanger = true;
/** /**
@ -277,7 +277,7 @@ public class GATKArgumentCollection {
if (other.numberOfThreads != this.numberOfThreads) { if (other.numberOfThreads != this.numberOfThreads) {
return false; return false;
} }
if (other.useLocusIteratorByState != this.useLocusIteratorByState) { if (other.useLocusIteratorByHanger != this.useLocusIteratorByHanger ) {
return false; return false;
} }

7
java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
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@ -100,9 +100,10 @@ public class AlignmentContext {
public String getContig() { return getLocation().getContig(); } public String getContig() { return getLocation().getContig(); }
public long getPosition() { return getLocation().getStart(); } public long getPosition() { return getLocation().getStart(); }
public GenomeLoc getLocation() { return loc; } public GenomeLoc getLocation() { return loc; }
public void setLocation(GenomeLoc loc) {
this.loc = loc.clone(); //public void setLocation(GenomeLoc loc) {
} // this.loc = loc.clone();
//}
public void downsampleToCoverage(int coverage) { public void downsampleToCoverage(int coverage) {
if ( numReads() <= coverage ) if ( numReads() <= coverage )

6
java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
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@ -61,10 +61,10 @@ public abstract class LocusView extends LocusIterator implements View {
Iterator<SAMRecord> reads = new FilteringIterator(provider.getReadIterator(), new LocusStreamFilterFunc()); Iterator<SAMRecord> reads = new FilteringIterator(provider.getReadIterator(), new LocusStreamFilterFunc());
this.sourceInfo = provider.getReadIterator().getSourceInfo(); this.sourceInfo = provider.getReadIterator().getSourceInfo();
if ( GenomeAnalysisEngine.instance != null && GenomeAnalysisEngine.instance.getArguments().useLocusIteratorByState) if ( GenomeAnalysisEngine.instance != null && GenomeAnalysisEngine.instance.getArguments().useLocusIteratorByHanger)
this.loci = new LocusIteratorByState(reads, sourceInfo);
else
this.loci = new LocusIteratorByHanger(reads, sourceInfo); this.loci = new LocusIteratorByHanger(reads, sourceInfo);
else
this.loci = new LocusIteratorByState(reads, sourceInfo);
seedNextLocus(); seedNextLocus();
provider.register(this); provider.register(this);

134
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -112,7 +112,7 @@ public class LocusIteratorByState extends LocusIterator {
//if ( cigarOffset == cigar.numCigarElements() ) //if ( cigarOffset == cigar.numCigarElements() )
// return null; // we are done // return null; // we are done
if (DEBUG2) System.out.printf("stepForwardOnGenome2: curElement=%s, counter=%d, len=%d%n", curElement, cigarElementCounter, curElement != null ? curElement.getLength() : -1); //if (DEBUG2) System.out.printf("stepForwardOnGenome2: curElement=%s, counter=%d, len=%d%n", curElement, cigarElementCounter, curElement != null ? curElement.getLength() : -1);
if ( curElement == null || ++cigarElementCounter >= curElement.getLength() ) { if ( curElement == null || ++cigarElementCounter >= curElement.getLength() ) {
cigarOffset++; cigarOffset++;
if ( cigarOffset < nCigarElements ) { if ( cigarOffset < nCigarElements ) {
@ -151,102 +151,15 @@ public class LocusIteratorByState extends LocusIterator {
default : throw new IllegalStateException("Case statement didn't deal with cigar op: " + curElement.getOperator()); default : throw new IllegalStateException("Case statement didn't deal with cigar op: " + curElement.getOperator());
} }
if (DEBUG2) System.out.printf("stepForwardOnGenome3: done=%b curElement=%s, counter=%d, len=%d, offset=%d%n", //if (DEBUG2) System.out.printf("stepForwardOnGenome3: done=%b curElement=%s, counter=%d, len=%d, offset=%d%n",
done, curElement, cigarElementCounter, curElement != null ? curElement.getLength() : -1, getReadOffset()); // done, curElement, cigarElementCounter, curElement != null ? curElement.getLength() : -1, getReadOffset());
return done ? curElement.getOperator() : stepForwardOnGenome(); return done ? curElement.getOperator() : stepForwardOnGenome();
} }
} }
/* private class SAMRecordState {
SAMRecord read;
int readOffset = -1; // how far are we offset from the start of the read bases?
int genomeOffset = -1; // how far are we offset from the alignment start on the genome?
Iterator<CigarElement> cigarIt = null;
CigarElement curElement = null;
int cigarElementCounter = 0;
public SAMRecordState(SAMRecord read) {
this.read = read;
cigarIt = read.getCigar().getCigarElements().iterator();
//stepForwardOnGenome(); // todo -- may be a performance issue -- can we avoid this?
}
public SAMRecord getRead() { return read; }
*//**
* What is our current offset in the read's bases that aligns us with the reference genome?
*
* @return
*//*
public int getReadOffset() { return readOffset; }
*//**
* What is the current offset w.r.t. the alignment state that aligns us to the readOffset?
*
* @return
*//*
public int getGenomeOffset() { return genomeOffset; }
public int getGenomePosition() { return read.getAlignmentStart() + getGenomeOffset(); }
public GenomeLoc getLocation() {
return GenomeLocParser.createGenomeLoc(read.getReferenceIndex(), getGenomePosition());
}
public CigarOperator getCurrentCigarOperator() { return curElement.getOperator(); }
public CigarOperator stepForwardOnGenome() {
if (DEBUG2) System.out.printf("stepForwardOnGenome1: cigarIt=%s%n", cigarIt);
if (cigarIt == null && ! cigarIt.hasNext())
return null; // we are done
if (DEBUG2) System.out.printf("stepForwardOnGenome2: curElement=%s, counter=%d, len=%d%n", curElement, cigarElementCounter, curElement != null ? curElement.getLength() : -1);
if ( curElement == null || ++cigarElementCounter >= curElement.getLength() ) {
if ( cigarIt.hasNext() ) {
curElement = cigarIt.next();
cigarElementCounter = 0;
} else {
return null;
}
}
boolean done = false;
switch (curElement.getOperator()) {
case H : // ignore hard clips
case P : // ignore pads
cigarElementCounter = curElement.getLength();
break;
case S : // soft clip
case I : // insertion w.r.t. the reference
// readOffset++; done = true; break;
cigarElementCounter = curElement.getLength();
readOffset += curElement.getLength();
break;
case N : // reference skip
cigarElementCounter = curElement.getLength();
genomeOffset += curElement.getLength();
break;
case D : // deletion w.r.t. the reference
genomeOffset++;
done = true;
break;
case M :
readOffset++;
genomeOffset++;
done = true;
break;
default : throw new IllegalStateException("Case statement didn't deal with cigar op: " + curElement.getOperator());
}
if (DEBUG2) System.out.printf("stepForwardOnGenome3: done=%b curElement=%s, counter=%d, len=%d, offset=%d%n",
done, curElement, cigarElementCounter, curElement != null ? curElement.getLength() : -1, getReadOffset());
return done ? curElement.getOperator() : stepForwardOnGenome();
}
}*/
private LinkedList<SAMRecordState> readStates = new LinkedList<SAMRecordState>(); private LinkedList<SAMRecordState> readStates = new LinkedList<SAMRecordState>();
final boolean DEBUG = false; //final boolean DEBUG = false;
final boolean DEBUG2 = false && DEBUG; //final boolean DEBUG2 = false && DEBUG;
private Reads readInfo; private Reads readInfo;
// ----------------------------------------------------------------------------------------------------------------- // -----------------------------------------------------------------------------------------------------------------
@ -269,7 +182,7 @@ public class LocusIteratorByState extends LocusIterator {
public boolean hasNext() { public boolean hasNext() {
boolean r = ! readStates.isEmpty() || it.hasNext(); boolean r = ! readStates.isEmpty() || it.hasNext();
if ( DEBUG ) System.out.printf("hasNext() = %b%n", r); //if ( DEBUG ) System.out.printf("hasNext() = %b%n", r);
return r; return r;
} }
@ -297,10 +210,10 @@ public class LocusIteratorByState extends LocusIterator {
// //
// ----------------------------------------------------------------------------------------------------------------- // -----------------------------------------------------------------------------------------------------------------
public AlignmentContext next() { public AlignmentContext next() {
if (DEBUG) { //if (DEBUG) {
logger.debug("in Next:"); // logger.debug("in Next:");
printState(); // printState();
} //}
collectPendingReads(readInfo.getMaxReadsAtLocus()); collectPendingReads(readInfo.getMaxReadsAtLocus());
@ -318,30 +231,28 @@ public class LocusIteratorByState extends LocusIterator {
updateReadStates(); // critical - must be called after we get the current state offsets and location updateReadStates(); // critical - must be called after we get the current state offsets and location
if (DEBUG) { //if (DEBUG) {
logger.debug("DONE WITH NEXT, updating read states, current state is:"); // logger.debug("DONE WITH NEXT, updating read states, current state is:");
printState(); // printState();
} //}
return new AlignmentContext(loc, reads, offsets); return new AlignmentContext(loc, reads, offsets);
} }
private void collectPendingReads(final int maximumPileupSize) { private void collectPendingReads(final int maximumPileupSize) {
if (DEBUG) { //if (DEBUG) {
logger.debug(String.format("entering collectPendingReads..., hasNext=%b", it.hasNext())); // logger.debug(String.format("entering collectPendingReads..., hasNext=%b", it.hasNext()));
printState(); // printState();
} //}
Boolean warned = false; // warn them once per locus Boolean warned = false; // warn them once per locus
int curSize = readStates.size(); // simple performance improvement -- avoids unnecessary size() operation int curSize = readStates.size(); // simple performance improvement -- avoids unnecessary size() operation
while (it.hasNext()) { while (it.hasNext()) {
SAMRecord read = it.next(); SAMRecord read = it.next();
if (DEBUG) logger.debug(String.format("Considering read %s: %s vs. %s", // if (DEBUG) logger.debug(String.format("Considering read %s: %s vs. %s",
read.getReadName(), getLocation(), GenomeLocParser.createGenomeLoc(read))); // read.getReadName(), getLocation(), GenomeLocParser.createGenomeLoc(read)));
//GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read);
//if (getLocation() != null && readLoc.distance(getLocation()) >= 1) {
if ( readIsPastCurrentPosition(read) ) { if ( readIsPastCurrentPosition(read) ) {
// We've collected up enough reads // We've collected up enough reads
it.pushback(read); it.pushback(read);
@ -357,7 +268,7 @@ public class LocusIteratorByState extends LocusIterator {
state.stepForwardOnGenome(); state.stepForwardOnGenome();
readStates.add(state); readStates.add(state);
curSize++; curSize++;
if (DEBUG) logger.debug(String.format(" ... added read %s", read.getReadName())); //if (DEBUG) logger.debug(String.format(" ... added read %s", read.getReadName()));
} }
} }
} }
@ -370,7 +281,6 @@ public class LocusIteratorByState extends LocusIterator {
else { else {
SAMRecordState state = readStates.getFirst(); SAMRecordState state = readStates.getFirst();
SAMRecord ourRead = state.getRead(); SAMRecord ourRead = state.getRead();
//System.out.printf("read=%d vs. us=%d%n", read.getAlignmentStart(), ourRead.getAlignmentStart());
return read.getReferenceIndex() > ourRead.getReferenceIndex() || read.getAlignmentStart() > state.getGenomePosition(); return read.getReferenceIndex() > ourRead.getReferenceIndex() || read.getAlignmentStart() > state.getGenomePosition();
} }
} }
@ -382,7 +292,7 @@ public class LocusIteratorByState extends LocusIterator {
SAMRecordState state = it.next(); SAMRecordState state = it.next();
CigarOperator op = state.stepForwardOnGenome(); CigarOperator op = state.stepForwardOnGenome();
if ( op == null ) { // we've stepped off the end of the object if ( op == null ) { // we've stepped off the end of the object
if (DEBUG) logger.debug(String.format(" removing read %s at %d", state.getRead().getReadName(), state.getRead().getAlignmentStart())); //if (DEBUG) logger.debug(String.format(" removing read %s at %d", state.getRead().getReadName(), state.getRead().getAlignmentStart()));
it.remove(); it.remove();
} }
} }

1
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -181,6 +181,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
//if ( eval!=null ) System.out.printf("Eval: %f %d %b%n", eval.getVariationConfidence(), minDiscoveryQ, eval.getVariationConfidence() < minDiscoveryQ); //if ( eval!=null ) System.out.printf("Eval: %f %d %b%n", eval.getVariationConfidence(), minDiscoveryQ, eval.getVariationConfidence() < minDiscoveryQ);
if ( eval != null ) { if ( eval != null ) {
// comment to disable variant filtering by confidence score
if ( evalContainsGenotypes ) { if ( evalContainsGenotypes ) {
// Genotyping - use best vs. next best lod // Genotyping - use best vs. next best lod
if ( eval.getConsensusConfidence() < minConfidenceScore ) eval = null; if ( eval.getConsensusConfidence() < minConfidenceScore ) eval = null;

2
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java
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@ -86,7 +86,7 @@ public class SAMBAMDataSourceTest extends BaseTest {
int count = 0; int count = 0;
// setup the data // setup the data
fl.add(new File(oneKGLocation + "/pilot3/sams/NA12892.bam")); fl.add(new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"));
Reads reads = new Reads(fl); Reads reads = new Reads(fl);
try { try {

3
python/MergeBAMBatch.py
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@ -65,8 +65,7 @@ if __name__ == "__main__":
if OPTIONS.ignoreExistingFiles or not os.path.exists(spec.getMergedBAM()): if OPTIONS.ignoreExistingFiles or not os.path.exists(spec.getMergedBAM()):
output = spec.getMergedBase() output = spec.getMergedBase()
cmd = spec.mergeCmd(OPTIONS.mergeBin, useSamtools = OPTIONS.useSamtools) cmd = spec.mergeCmd(OPTIONS.mergeBin, useSamtools = OPTIONS.useSamtools)
#print cmd jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, None, just_print_commands = OPTIONS.dry)
jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, output, just_print_commands = OPTIONS.dry)
if OPTIONS.ignoreExistingFiles or not os.path.exists(spec.getMergedBAMIndex()): if OPTIONS.ignoreExistingFiles or not os.path.exists(spec.getMergedBAMIndex()):
jobid = farm_commands.cmd(spec.getIndexCmd(), OPTIONS.farmQueue, None, waitID = jobid, just_print_commands = OPTIONS.dry) jobid = farm_commands.cmd(spec.getIndexCmd(), OPTIONS.farmQueue, None, waitID = jobid, just_print_commands = OPTIONS.dry)