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cleanup of the pile-up limit exceeded warning, and a little code cleanup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2657 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-01-21 22:17:24 +00:00
parent de21943acd
commit cc3b818268
1 changed files with 10 additions and 8 deletions
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20
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -448,7 +448,7 @@ public class LocusIteratorByState extends LocusIterator {
// logger.debug(String.format("entering collectPendingReads..., hasNext=%b", it.hasNext())); // logger.debug(String.format("entering collectPendingReads..., hasNext=%b", it.hasNext()));
// printState(); // printState();
//} //}
GenomeLoc location = null;
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();
@ -464,10 +464,13 @@ public class LocusIteratorByState extends LocusIterator {
curSize++; curSize++;
if (state.hadIndel()) hasExtendedEvents = true; if (state.hadIndel()) hasExtendedEvents = true;
//if (DEBUG) logger.debug(String.format(" ... added read %s", read.getReadName())); //if (DEBUG) logger.debug(String.format(" ... added read %s", read.getReadName()));
} else if (location == null) {
location = GenomeLocParser.createGenomeLoc(read);
}
} }
} }
overflowTracker.exceeded(read, curSize); if (location != null) overflowTracker.exceeded(location, curSize);
}
} }
// fast testing of position // fast testing of position
@ -560,16 +563,15 @@ class LocusOverflowTracker {
/** /**
* have we exceeded the maximum pile-up size? * have we exceeded the maximum pile-up size?
* *
* @param read the current read, we use this to get the GenomeLoc only if needed (for efficiency) * @param loc the current location
* @param pileupSize the pile-up size * @param pileupSize the pile-up size
* *
* @return return true if we're greater, false if we're not * @return return true if we're greater, false if we're not
*/ */
public boolean exceeded(SAMRecord read, int pileupSize) { public boolean exceeded(GenomeLoc loc, int pileupSize) {
boolean exceeded = pileupSize >= maxPileupSize; boolean exceeded = pileupSize >= maxPileupSize;
if (exceeded) { if (exceeded && warningsEmitted <= MAX_WARNINGS) {
warningInQueue = true; warningInQueue = true;
GenomeLoc loc = GenomeLocParser.createGenomeLoc(read);
if (lastLocation == null) lastLocation = loc; if (lastLocation == null) lastLocation = loc;
else if (lastLocation.contiguousP(loc)) else if (lastLocation.contiguousP(loc))
lastLocation = lastLocation.merge(loc); lastLocation = lastLocation.merge(loc);
@ -598,10 +600,10 @@ class LocusOverflowTracker {
warningInQueue = false; warningInQueue = false;
if (warningsEmitted < MAX_WARNINGS) { if (warningsEmitted < MAX_WARNINGS) {
warningsEmitted++; warningsEmitted++;
Utils.warnUser("Unable to add a read, we're over the hanger limit of " + maxPileupSize + " at location " + lastLocation); Utils.warnUser("Unable to add a reads to the pile-up, we're over the hanger limit of " + maxPileupSize + " at location: " + lastLocation);
} else if (warningsEmitted == MAX_WARNINGS) { } else if (warningsEmitted == MAX_WARNINGS) {
warningsEmitted++; warningsEmitted++;
Utils.warnUser("Unable to add a read, we're over the hanger limit of " + maxPileupSize + " at location " + lastLocation + Utils.warnUser("Unable to add a reads to the pile-up, we're over the hanger limit of " + maxPileupSize + " at location: " + lastLocation +
"; the maximum warning count has been reached, we will no longer emit warnings of this nature!!"); "; the maximum warning count has been reached, we will no longer emit warnings of this nature!!");
} }
} }