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 21fb4247e..e88a3cdcf 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -643,18 +643,13 @@ public class IndelRealigner extends ReadWalker { // TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM 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; // 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); @@ -709,11 +704,6 @@ 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!! @@ -882,6 +872,11 @@ public class IndelRealigner extends ReadWalker { 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); // first, move existing indels (for 1 indel reads only) to leftmost position within identical sequence