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Redid fix for corner case when forming consensus with reads that start/end with insertions and that don't agree with each other in inserted bases: since I can't iterate over the elements of a HashMap because keys might change during iteration, and since I can't use ConcurrentHashMaps, the code now copies structure of (bases, number of times seen) into ArrayList, which can be addressed by element index in order to iterate on it.

This commit is contained in:
Guillermo del Angel 2012-02-20 09:12:51 -05:00
parent fe102a5d47
commit 0f5674b95e
1 changed files with 46 additions and 31 deletions
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77
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -37,6 +37,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
import org.broadinstitute.sting.utils.pileup.PileupElement;
@ -141,62 +142,76 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
String indelString = p.getEventBases();
if (p.isInsertion()) {
boolean foundKey = false;
// copy of hashmap into temp arrayList
ArrayList<Pair<String,Integer>> cList = new ArrayList<Pair<String,Integer>>();
for (String s : consensusIndelStrings.keySet()) {
cList.add(new Pair<String, Integer>(s,consensusIndelStrings.get(s)));
}
if (read.getAlignmentEnd() == loc.getStart()) {
// first corner condition: a read has an insertion at the end, and we're right at the insertion.
// In this case, the read could have any of the inserted bases and we need to build a consensus
for (String s : consensusIndelStrings.keySet()) {
int cnt = consensusIndelStrings.get(s);
for (int k=0; k < cList.size(); k++) {
String s = cList.get(k).getFirst();
int cnt = cList.get(k).getSecond();
// case 1: current insertion is prefix of indel in hash map
if (s.startsWith(indelString)) {
// case 1: current insertion is prefix of indel in hash map
consensusIndelStrings.put(s, cnt + 1);
cList.set(k,new Pair<String, Integer>(s,cnt+1));
foundKey = true;
break;
} else if (indelString.startsWith(s)) {
}
else if (indelString.startsWith(s)) {
// case 2: indel stored in hash table is prefix of current insertion
// In this case, new bases are new key.
consensusIndelStrings.remove(s);
consensusIndelStrings.put(indelString, cnt + 1);
foundKey = true;
break;
cList.set(k,new Pair<String, Integer>(indelString,cnt+1));
}
}
if (!foundKey)
// none of the above: event bases not supported by previous table, so add new key
consensusIndelStrings.put(indelString, 1);
cList.add(new Pair<String, Integer>(indelString,1));
} else if (read.getAlignmentStart() == loc.getStart() + 1) {
}
else if (read.getAlignmentStart() == loc.getStart()+1) {
// opposite corner condition: read will start at current locus with an insertion
for (String s : consensusIndelStrings.keySet()) {
int cnt = consensusIndelStrings.get(s);
for (int k=0; k < cList.size(); k++) {
String s = cList.get(k).getFirst();
int cnt = cList.get(k).getSecond();
if (s.endsWith(indelString)) {
// case 1: current insertion is suffix of indel in hash map
consensusIndelStrings.put(s, cnt + 1);
// case 1: current insertion (indelString) is suffix of indel in hash map (s)
cList.set(k,new Pair<String, Integer>(s,cnt+1));
foundKey = true;
break;
} else if (indelString.endsWith(s)) {
// case 2: indel stored in hash table is suffix of current insertion
}
else if (indelString.endsWith(s)) {
// case 2: indel stored in hash table is prefix of current insertion
// In this case, new bases are new key.
consensusIndelStrings.remove(s);
consensusIndelStrings.put(indelString, cnt + 1);
foundKey = true;
break;
cList.set(k,new Pair<String, Integer>(indelString,cnt+1));
}
}
if (!foundKey)
// none of the above: event bases not supported by previous table, so add new key
consensusIndelStrings.put(indelString, 1);
cList.add(new Pair<String, Integer>(indelString,1));
} else {
// normal case: insertion somewhere in the middle of a read: add count to hash map
int cnt = consensusIndelStrings.containsKey(indelString) ? consensusIndelStrings.get(indelString) : 0;
consensusIndelStrings.put(indelString, cnt + 1);
}
else {
// normal case: insertion somewhere in the middle of a read: add count to arrayList
int cnt = consensusIndelStrings.containsKey(indelString)? consensusIndelStrings.get(indelString):0;
cList.add(new Pair<String, Integer>(indelString,cnt+1));
}
} else if (p.isDeletion()) {
indelString = String.format("D%d", p.getEventLength());
int cnt = consensusIndelStrings.containsKey(indelString) ? consensusIndelStrings.get(indelString) : 0;
consensusIndelStrings.put(indelString, cnt + 1);
// copy back arrayList into hashMap
consensusIndelStrings.clear();
for (Pair<String,Integer> pair : cList) {
consensusIndelStrings.put(pair.getFirst(),pair.getSecond());
}
}
else if (p.isDeletion()) {
indelString = String.format("D%d",p.getEventLength());
int cnt = consensusIndelStrings.containsKey(indelString)? consensusIndelStrings.get(indelString):0;
consensusIndelStrings.put(indelString,cnt+1);
}
}