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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-08-16 16:26:33 -04:00
parent 946f5c53fe 6e828260a0
commit 5f3f46aad1
5 changed files with 15 additions and 24 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
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@ -96,24 +96,23 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
loadArgumentsIntoObject(walker);
argumentSources.add(walker);
Collection<RMDTriplet> newStyle = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
Collection<RMDTriplet> rodBindings = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
// todo: remove me when the old style system is removed
if ( getArgumentCollection().RODBindings.size() > 0 ) {
logger.warn("################################################################################");
logger.warn("################################################################################");
logger.warn("Deprecated -B rod binding syntax detected. This syntax will be retired in GATK 1.2.");
logger.warn("Deprecated -B rod binding syntax detected. This syntax has been eliminated in GATK 1.2.");
logger.warn("Please use arguments defined by each specific walker instead.");
for ( String oldStyleRodBinding : getArgumentCollection().RODBindings ) {
logger.warn(" -B rod binding with value " + oldStyleRodBinding + " tags: " + parser.getTags(oldStyleRodBinding).getPositionalTags());
}
logger.warn("################################################################################");
logger.warn("################################################################################");
System.exit(1);
}
Collection<RMDTriplet> oldStyle = ListFileUtils.unpackRODBindingsOldStyle(getArgumentCollection().RODBindings, parser);
oldStyle.addAll(newStyle);
engine.setReferenceMetaDataFiles(oldStyle);
engine.setReferenceMetaDataFiles(rodBindings);
for (ReadFilter filter: filters) {
loadArgumentsIntoObject(filter);

10
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -101,6 +101,8 @@ public class GATKArgumentCollection {
@Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
public File referenceFile = null;
@Deprecated
@Hidden
@ElementList(required = false)
@Input(fullName = "rodBind", shortName = "B", doc = "Bindings for reference-ordered data, in the form :<name>,<type> <file>", required = false)
public ArrayList<String> RODBindings = new ArrayList<String>();
@ -340,14 +342,6 @@ public class GATKArgumentCollection {
return false;
}
}
if (other.RODBindings.size() != RODBindings.size()) {
return false;
}
for (int x = 0; x < RODBindings.size(); x++) {
if (!RODBindings.get(x).equals(other.RODBindings.get(x))) {
return false;
}
}
if (!other.samFiles.equals(this.samFiles)) {
return false;
}

7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -484,6 +484,9 @@ public class UnifiedGenotyperEngine {
Map<String, AlignmentContext> stratifiedContexts = null;
if ( !BaseUtils.isRegularBase( refContext.getBase() ) )
return null;
if ( model == GenotypeLikelihoodsCalculationModel.Model.INDEL ) {
if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
@ -498,6 +501,7 @@ public class UnifiedGenotyperEngine {
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
} else {
// todo - tmp will get rid of extended events so this wont be needed
if (!rawContext.hasExtendedEventPileup())
return null;
@ -515,9 +519,6 @@ public class UnifiedGenotyperEngine {
}
} else if ( model == GenotypeLikelihoodsCalculationModel.Model.SNP ) {
if ( !BaseUtils.isRegularBase( refContext.getBase() ) )
return null;
// stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE);

5
public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
View File

@ -135,6 +135,11 @@ public class NWaySAMFileWriter implements SAMFileWriter {
public void addAlignment(SAMRecord samRecord) {
final SAMReaderID id = toolkit.getReaderIDForRead(samRecord);
String rg = samRecord.getStringAttribute("RG");
if ( rg != null ) {
String rg_orig = toolkit.getReadsDataSource().getOriginalReadGroupId(rg);
samRecord.setAttribute("RG",rg_orig);
}
writerMap.get(id).addAlignment(samRecord);
}

8
public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
View File

@ -88,14 +88,6 @@ public class GATKArgumentCollectionUnitTest extends BaseTest {
collect.intervals.add("intervals".toLowerCase());
collect.excludeIntervals = new ArrayList<String>();
collect.numberOfThreads = 1;
// make some rod bindings up
ArrayList<String> fakeBindings = new ArrayList<String>();
fakeBindings.add("Bind1");
fakeBindings.add("Bind2");
fakeBindings.add("Bind3");
collect.RODBindings = fakeBindings;
}