diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 484981e44..21fb4247e 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -641,16 +641,31 @@ public class IndelRealigner extends ReadWalker { // 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 iter = altConsenses.iterator(); @@ -694,6 +709,11 @@ public class IndelRealigner extends ReadWalker { 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!!