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Better method for downsampling deep regions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@983 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-11 16:57:40 +00:00
parent 4d9a88153a
commit 599ceeddd8
1 changed files with 16 additions and 5 deletions
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21
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -271,9 +271,20 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// if we have too many reads with mismatches, be greedy // if we have too many reads with mismatches, be greedy
if ( altReads.size() > GREEDY_THRESHOLD) { if ( altReads.size() > GREEDY_THRESHOLD) {
logger.debug("Downsampling from " + altReads.size() + " to " + GREEDY_THRESHOLD + " mismatching reads"); logger.debug("Downsampling from " + altReads.size() + " to " + GREEDY_THRESHOLD + " mismatching reads");
//sortByGreedy(); // the best thing to do here is to randomly sample from the reads
for ( int i = GREEDY_THRESHOLD; i < altReads.size(); i++) // however, we definitely do want to keep the clean indel-containing reads
altAlignmentsToTest.set(i, false); // (which were purposely placed at the beginning of the list)
int downsampleTo = GREEDY_THRESHOLD - priorIndelsToTest.size();
int sampleRate = (altReads.size() - priorIndelsToTest.size()) / downsampleTo;
for ( int i = 0; i < downsampleTo; i++) {
int index = priorIndelsToTest.size() + (i * sampleRate);
for ( int j = 1; j < sampleRate; j++)
altAlignmentsToTest.set(index+j, false);
}
// also get the trailing reads
int tail = priorIndelsToTest.size() + (downsampleTo * sampleRate);
for ( int i = tail; i < altAlignmentsToTest.size(); i++)
altAlignmentsToTest.set(i, false);
} }
Consensus bestConsensus = null; Consensus bestConsensus = null;
@ -710,7 +721,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// got maximum possible shift after checking period=1 above. // got maximum possible shift after checking period=1 above.
} }
// if ( ce2.getLength() >= 2 ) // if ( ce2.getLength() >= 2 )
// System.out.println("-----------------------------------\n FROM:\n"+AlignmentUtils.alignmentToString(cigar,readSeq,refSeq,refIndex, (readIsConsensusSequence?refIndex:0))); // System.out.println("-----------------------------------\n FROM:\n"+AlignmentUtils.alignmentToString(cigar,readSeq,refSeq,refIndex, (readIsConsensusSequence?refIndex:0)));
@ -720,7 +731,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
newCigar.add(ce2); newCigar.add(ce2);
newCigar.add(new CigarElement(cigar.getCigarElement(2).getLength()+difference, CigarOperator.M)); newCigar.add(new CigarElement(cigar.getCigarElement(2).getLength()+difference, CigarOperator.M));
// System.out.println(" FROM:\n"+AlignmentUtils.alignmentToString(cigar,readSeq,refSeq,refIndex)); // System.out.println(" FROM:\n"+AlignmentUtils.alignmentToString(cigar,readSeq,refSeq,refIndex));
// if ( ce2.getLength() >=2 ) // if ( ce2.getLength() >=2 )
// System.out.println(" REALIGNED TO:\n"+AlignmentUtils.alignmentToString(newCigar,readSeq,refSeq,refIndex,readIndex)+"\n"); // System.out.println(" REALIGNED TO:\n"+AlignmentUtils.alignmentToString(newCigar,readSeq,refSeq,refIndex,readIndex)+"\n");
logger.debug("Realigning indel: " + cigarToString(cigar) + " to " + cigarToString(newCigar)); logger.debug("Realigning indel: " + cigarToString(cigar) + " to " + cigarToString(newCigar));