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fixed locus pile-up limiting problem 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1505 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-09-02 16:56:44 +00:00
parent d8aff9a925
commit 0e6feff8f2
1 changed files with 48 additions and 46 deletions
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72
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java
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@ -60,6 +60,7 @@ public class LocusIteratorByHanger extends LocusIterator {
final boolean DEBUG = false; final boolean DEBUG = false;
boolean justCleared = false; boolean justCleared = false;
private Reads readInfo; private Reads readInfo;
// ----------------------------------------------------------------------------------------------------------------- // -----------------------------------------------------------------------------------------------------------------
// //
// constructors and other basic operations // constructors and other basic operations
@ -83,15 +84,15 @@ public class LocusIteratorByHanger extends LocusIterator {
} }
public void printState() { public void printState() {
for ( int i = 0; i < readHanger.size(); i++ ) { for (int i = 0; i < readHanger.size(); i++) {
RefHanger.Hanger rhanger = readHanger.getHanger(i); RefHanger.Hanger rhanger = readHanger.getHanger(i);
RefHanger.Hanger ohanger = offsetHanger.getHanger(i); RefHanger.Hanger ohanger = offsetHanger.getHanger(i);
logger.debug(String.format("printState(): location %s", rhanger.loc)); logger.debug(String.format("printState(): location %s", rhanger.loc));
for ( int j = 0; j < rhanger.size(); j++ ) { for (int j = 0; j < rhanger.size(); j++) {
SAMRecord read = (SAMRecord)rhanger.get(j); SAMRecord read = (SAMRecord) rhanger.get(j);
int offset = (Integer)ohanger.get(j); int offset = (Integer) ohanger.get(j);
logger.debug(String.format(" read: %s(%d)=%s", read.getReadName(), offset, read.getReadString().charAt(offset) )); logger.debug(String.format(" read: %s(%d)=%s", read.getReadName(), offset, read.getReadString().charAt(offset)));
} }
} }
} }
@ -108,10 +109,10 @@ public class LocusIteratorByHanger extends LocusIterator {
// //
// ----------------------------------------------------------------------------------------------------------------- // -----------------------------------------------------------------------------------------------------------------
public AlignmentContext next() { public AlignmentContext next() {
if ( ! currentPositionIsFullyCovered() ) if (!currentPositionIsFullyCovered())
expandWindow(INCREMENT_SIZE,readInfo.getMaxReadsAtLocus()); expandWindow(INCREMENT_SIZE, readInfo.getMaxReadsAtLocus());
if ( DEBUG ) { if (DEBUG) {
logger.debug("in Next:"); logger.debug("in Next:");
printState(); printState();
} }
@ -119,7 +120,7 @@ public class LocusIteratorByHanger extends LocusIterator {
RefHanger.Hanger rhanger = readHanger.popLeft(); RefHanger.Hanger rhanger = readHanger.popLeft();
RefHanger.Hanger ohanger = offsetHanger.popLeft(); RefHanger.Hanger ohanger = offsetHanger.popLeft();
if ( rhanger.size() == 0 ) { if (rhanger.size() == 0) {
// we are in the case where there are no reads (we're inside a large indel without any reads // we are in the case where there are no reads (we're inside a large indel without any reads
// so recursively call next. This is safe because having a position without any reads // so recursively call next. This is safe because having a position without any reads
// implies that there are positions to the right with reads // implies that there are positions to the right with reads
@ -130,26 +131,36 @@ public class LocusIteratorByHanger extends LocusIterator {
} }
} }
protected void hangRead(final SAMRecord read) { protected boolean hangRead(final SAMRecord read, final int maximumPileupSize, boolean warned) {
GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read); GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read);
for ( AlignmentBlock block : read.getAlignmentBlocks() ) { for (AlignmentBlock block : read.getAlignmentBlocks()) {
if ( DEBUG ) logger.debug(String.format("Processing block %s len=%d", block, block.getLength())); if (DEBUG) logger.debug(String.format("Processing block %s len=%d", block, block.getLength()));
for ( int i = 0; i < block.getLength(); i++ ) { for (int i = 0; i < block.getLength(); i++) {
// check to see if we've exceeded the maximum number of reads in the pile-up
GenomeLoc offset = GenomeLocParser.createGenomeLoc(readLoc.getContigIndex(), block.getReferenceStart() + i); GenomeLoc offset = GenomeLocParser.createGenomeLoc(readLoc.getContigIndex(), block.getReferenceStart() + i);
int hangerSize = (readHanger.hasLocation(offset)) ? readHanger.getHanger(offset).size() : -1;
if (hangerSize >= maximumPileupSize) {
if (!warned) {
warned = true;
Utils.warnUser("Unable to add a read, we're over the hanger limit of " + maximumPileupSize + " at location " + readHanger.getLeftLoc());
}
} else {
readHanger.expandingPut(offset, read); readHanger.expandingPut(offset, read);
offsetHanger.expandingPut(offset, block.getReadStart() + i - 1); offsetHanger.expandingPut(offset, block.getReadStart() + i - 1);
if ( DEBUG ) logger.debug(String.format(" # Added %s", offset)); }
if (DEBUG) logger.debug(String.format(" # Added %s", offset));
} }
} }
return warned; // did we warn the user about this location?
} }
private final boolean currentPositionIsFullyCovered(final GenomeLoc nextReadInStreamLoc) { private final boolean currentPositionIsFullyCovered(final GenomeLoc nextReadInStreamLoc) {
if ( readHanger.isEmpty() ) if (readHanger.isEmpty())
// If the buffer is empty, we're definitely not done // If the buffer is empty, we're definitely not done
return false; return false;
if ( nextReadInStreamLoc.compareTo(readHanger.getLeftLoc()) == 1 ) if (nextReadInStreamLoc.compareTo(readHanger.getLeftLoc()) == 1)
// the next read in the stream is beyond the left most position, so it's fully covered // the next read in the stream is beyond the left most position, so it's fully covered
return true; return true;
else else
@ -158,7 +169,7 @@ public class LocusIteratorByHanger extends LocusIterator {
} }
private final boolean currentPositionIsFullyCovered() { private final boolean currentPositionIsFullyCovered() {
if ( ! it.hasNext() ) // if there are no more reads, we are fully covered if (!it.hasNext()) // if there are no more reads, we are fully covered
return true; return true;
else { else {
final SAMRecord read = it.peek(); final SAMRecord read = it.peek();
@ -171,17 +182,17 @@ public class LocusIteratorByHanger extends LocusIterator {
private final void expandWindow(final int incrementSize, final int maximumPileupSize) { private final void expandWindow(final int incrementSize, final int maximumPileupSize) {
// todo: reenable // todo: reenable
if ( false && incrementSize != 1 ) { if (false && incrementSize != 1) {
Utils.scareUser(String.format("BUG: IncrementSize=%d != 1, the codebase doesn't support this extension strategy yet", incrementSize)); Utils.scareUser(String.format("BUG: IncrementSize=%d != 1, the codebase doesn't support this extension strategy yet", incrementSize));
} }
if ( DEBUG ) { if (DEBUG) {
logger.debug(String.format("entering expandWindow..., hasNext=%b", it.hasNext())); logger.debug(String.format("entering expandWindow..., hasNext=%b", it.hasNext()));
printState(); printState();
} }
boolean warned = false; // warn them once per locus Boolean warned = false; // warn them once per locus
while ( it.hasNext() ) { while (it.hasNext()) {
if ( DEBUG ) { if (DEBUG) {
logger.debug(String.format("Expanding window")); logger.debug(String.format("Expanding window"));
printState(); printState();
} }
@ -190,7 +201,7 @@ public class LocusIteratorByHanger extends LocusIterator {
justCleared = false; justCleared = false;
GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read); GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read);
if ( DEBUG ) { if (DEBUG) {
logger.debug(String.format(" Expanding window sizes %d with %d : left=%s, right=%s, readLoc = %s, cmp=%d", logger.debug(String.format(" Expanding window sizes %d with %d : left=%s, right=%s, readLoc = %s, cmp=%d",
readHanger.size(), incrementSize, readHanger.size(), incrementSize,
readHanger.hasHangers() ? readHanger.getLeftLoc() : "NA", readHanger.hasHangers() ? readHanger.getLeftLoc() : "NA",
@ -200,21 +211,12 @@ public class LocusIteratorByHanger extends LocusIterator {
} }
//if ( readHanger.size() >= incrementSize ) { //if ( readHanger.size() >= incrementSize ) {
//if ( readHanger.hasHangers() && readLoc.compareTo(readHanger.getLeftLoc()) == 1) { //if ( readHanger.hasHangers() && readLoc.compareTo(readHanger.getLeftLoc()) == 1) {
if ( readHanger.hasHangers() && readLoc.distance(readHanger.getLeftLoc()) >= incrementSize ) { if (readHanger.hasHangers() && readLoc.distance(readHanger.getLeftLoc()) >= incrementSize) {
// We've collected up enough reads // We've collected up enough reads
it.pushback(read); it.pushback(read);
break; break;
} } else
else warned = hangRead(read,maximumPileupSize,warned);
// check to see if we've exceeded the maximum number of reads in the pile-up
if (readHanger.size() < maximumPileupSize)
hangRead(read);
else {
// if we haven't warned the user for this locus, do so now
if (!warned)
Utils.warnUser("Unable to add a read, we're over the hanger limit of " + maximumPileupSize + " at location " + readHanger.getLeftLoc());
warned = true;
}
} }
} }