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

public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -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);
+            engine.setReferenceMetaDataFiles(rodBindings);
-            oldStyle.addAll(newStyle);
-            engine.setReferenceMetaDataFiles(oldStyle);
 
             for (ReadFilter filter: filters) {
                 loadArgumentsIntoObject(filter);

public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -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;
         }

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

@@ -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);
 

public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java

@@ -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);
     }
 

public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java

@@ -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;
     }