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Ugh - backed out experimental code not for public consumption unintendedly committed

This commit is contained in:
Guillermo del Angel 2011-07-02 16:58:57 -04:00
parent c6c0dba040
commit 09af6bbc6c
2 changed files with 4 additions and 9 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -157,10 +157,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead()); GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
if (read == null) if (read == null)
continue; continue;
/* if(ReadUtils.is454Read(read)) { if(ReadUtils.is454Read(read)) {
continue; continue;
} }
*/
if (DEBUG && p.isIndel()) { if (DEBUG && p.isIndel()) {
System.out.format("Read: %s, cigar: %s, aln start: %d, aln end: %d, p.len:%d, Type:%s, EventBases:%s\n", System.out.format("Read: %s, cigar: %s, aln start: %d, aln end: %d, p.len:%d, Type:%s, EventBases:%s\n",
read.getReadName(),read.getCigar().toString(),read.getAlignmentStart(),read.getAlignmentEnd(), read.getReadName(),read.getCigar().toString(),read.getAlignmentStart(),read.getAlignmentEnd(),

9
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -105,7 +105,6 @@ public class PairHMMIndelErrorModel {
private static final double MIN_GAP_CONT_PENALTY = 10.0; private static final double MIN_GAP_CONT_PENALTY = 10.0;
private static final double GAP_PENALTY_HRUN_STEP = 1.0; // each increase in hrun decreases gap penalty by this. private static final double GAP_PENALTY_HRUN_STEP = 1.0; // each increase in hrun decreases gap penalty by this.
private static final double GOP_454_DELTA = 15.0; // lower gap penalty for 454 reads
private boolean doViterbi = false; private boolean doViterbi = false;
@ -772,10 +771,10 @@ public class PairHMMIndelErrorModel {
if (read == null) if (read == null)
continue; continue;
/* if(ReadUtils.is454Read(read) && !getGapPenaltiesFromFile) { if(ReadUtils.is454Read(read) && !getGapPenaltiesFromFile) {
continue; continue;
} }
*/
double[] recalQuals = null; double[] recalQuals = null;
/* /*
@ -991,10 +990,6 @@ public class PairHMMIndelErrorModel {
} else { } else {
currentContextGOP = Arrays.copyOfRange(gapOpenProbabilityMap.get(a), (int)indStart, (int)indStop); currentContextGOP = Arrays.copyOfRange(gapOpenProbabilityMap.get(a), (int)indStart, (int)indStop);
currentContextGCP = Arrays.copyOfRange(gapContProbabilityMap.get(a), (int)indStart, (int)indStop); currentContextGCP = Arrays.copyOfRange(gapContProbabilityMap.get(a), (int)indStart, (int)indStop);
if(ReadUtils.is454Read(read)) {
for (int k=0; k <currentContextGOP.length; k++ )
currentContextGOP[k] += GOP_454_DELTA/10;
}
readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, currentContextGOP, currentContextGCP); readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, currentContextGOP, currentContextGCP);
} }
} }