zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Adding debug statements for David to aid in testing the non-determinism problem. I wouldn't recommend running with --stats temporarily (or ever in fact, which is why it's @Hidden). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5907 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-05-31 19:53:59 +00:00
parent c50d290133
commit b75583a90b
1 changed files with 20 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -641,16 +641,31 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// if there are any known indels for this region, get them and create alternate consenses
generateAlternateConsensesFromKnownIndels(altConsenses, leftmostIndex, reference);
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) {
logger.warn("ERIC: altConsenses.size() after seeing known indels = " + altConsenses.size());
}
// decide which reads potentially need to be cleaned;
// if there are reads with a single indel in them, add that indel to the list of alternate consenses
long totalRawMismatchSum = determineReadsThatNeedCleaning(reads, refReads, altReads, altAlignmentsToTest, altConsenses, leftmostIndex, reference);
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) {
logger.warn("ERIC: altAlignmentsToTest.size() = " + altAlignmentsToTest.size());
}
// use 'Smith-Waterman' to create alternate consenses from reads that mismatch the reference, using totalRawMismatchSum as the random seed
if ( !USE_KNOWN_INDELS_ONLY && !NO_SW )
generateAlternateConsensesFromReads(altAlignmentsToTest, altConsenses, reference, leftmostIndex);
// if ( debugOn ) System.out.println("------\nChecking consenses...\n--------\n");
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) {
logger.warn("ERIC: altConsenses.size() after seeing reads = " + altConsenses.size());
}
Consensus bestConsensus = null;
Iterator<Consensus> iter = altConsenses.iterator();
@ -694,6 +709,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
break;
}
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) {
logger.warn("ERIC: bestConsensus = " + bestConsensus + ", this consensus = " + consensus);
}
//logger.debug("Mismatch sum of new consensus: " + consensus.mismatchSum);
if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
// we do not need this alt consensus, release memory right away!!