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Next version of test output for non-determinism 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5916 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-06-01 19:36:56 +00:00
parent 511cd48d7a
commit 81d9808eea
1 changed files with 6 additions and 11 deletions
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17
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -643,18 +643,13 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM // TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) { if ( OUT_STATS != null ) {
logger.warn("ERIC: altConsenses.size() after seeing known indels = " + altConsenses.size()); logger.warn("ERIC: reads.size() = " + reads.size());
} }
// decide which reads potentially need to be cleaned; // 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 // 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); 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 // 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 ) if ( !USE_KNOWN_INDELS_ONLY && !NO_SW )
generateAlternateConsensesFromReads(altAlignmentsToTest, altConsenses, reference, leftmostIndex); generateAlternateConsensesFromReads(altAlignmentsToTest, altConsenses, reference, leftmostIndex);
@ -709,11 +704,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
break; 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); //logger.debug("Mismatch sum of new consensus: " + consensus.mismatchSum);
if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) { if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
// we do not need this alt consensus, release memory right away!! // we do not need this alt consensus, release memory right away!!
@ -882,6 +872,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
continue; continue;
} }
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) {
logger.warn("ERIC: read = " + read.getReadName() + " " + read.getCigarString());
}
final AlignedRead aRead = new AlignedRead(read); final AlignedRead aRead = new AlignedRead(read);
// first, move existing indels (for 1 indel reads only) to leftmost position within identical sequence // first, move existing indels (for 1 indel reads only) to leftmost position within identical sequence