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1) Fix for Tim et al: HashMaps don't necessarily return objects in a deterministic fashion when keys are pointers; break it apart into a list. 

2) Fix for Kiran: when running with -Ddisable.help=true, don't exception out when trying to get the GATK version.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5154 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-02-01 06:06:48 +00:00
parent 5279ef24a3
commit 4243f0dea7
1 changed files with 12 additions and 7 deletions
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19
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -184,7 +184,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// the reads and known indels that fall into the current interval
private final ReadBin readsToClean = new ReadBin();
private final ArrayList<SAMRecord> readsNotToClean = new ArrayList<SAMRecord>();
private final IdentityHashMap<Object, VariantContext> knownIndelsToTry = new IdentityHashMap<Object, VariantContext>();
private final ArrayList<VariantContext> knownIndelsToTry = new ArrayList<VariantContext>();
private final HashSet<Object> indelRodsSeen = new HashSet<Object>();
private static final int MAX_QUAL = 99;
@ -366,7 +367,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( !NO_PG_TAG ) {
final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
programRecord.setProgramVersion(headerInfo.getString("org.broadinstitute.sting.gatk.version"));
try {
final String version = headerInfo.getString("org.broadinstitute.sting.gatk.version");
programRecord.setProgramVersion(version);
} catch (MissingResourceException e) {}
programRecord.setCommandLine(getToolkit().createApproximateCommandLineArgumentString(getToolkit(), this));
List<SAMProgramRecord> oldRecords = header.getProgramRecords();
@ -475,6 +479,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
private void cleanAndCallMap(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
clean(readsToClean);
knownIndelsToTry.clear();
indelRodsSeen.clear();
emit(readsNotToClean);
emit(readsToClean.getReads());
@ -507,6 +512,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( readsToClean.size() > 0 || readsNotToClean.size() > 0 ) {
clean(readsToClean);
knownIndelsToTry.clear();
indelRodsSeen.clear();
// merge the two sets for emission
readsNotToClean.addAll(readsToClean.getReads());
@ -557,12 +563,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
Iterator<GATKFeature> rodIter = rods.iterator();
while ( rodIter.hasNext() ) {
Object rod = rodIter.next().getUnderlyingObject();
if ( knownIndelsToTry.containsKey(rod) )
if ( indelRodsSeen.contains(rod) )
continue;
indelRodsSeen.add(rod);
if ( VariantContextAdaptors.canBeConvertedToVariantContext(rod))
knownIndelsToTry.put(rod, VariantContextAdaptors.toVariantContext("", rod, ref));
else
knownIndelsToTry.put(rod, null);
knownIndelsToTry.add(VariantContextAdaptors.toVariantContext("", rod, ref));
}
}
}
@ -794,7 +799,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
private void generateAlternateConsensesFromKnownIndels(final Set<Consensus> altConsensesToPopulate, final int leftmostIndex, final byte[] reference) {
for ( VariantContext knownIndel : knownIndelsToTry.values() ) {
for ( VariantContext knownIndel : knownIndelsToTry ) {
if ( knownIndel == null || !knownIndel.isIndel() )
continue;
byte[] indelStr = knownIndel.isInsertion() ? knownIndel.getAlternateAllele(0).getBases() : Utils.dupBytes((byte)'-', knownIndel.getReference().length());