Support for --assume-single-sample in UG, better malformated bam exceptions, and ignoring out of order contigs in seqdictutils. All for the CG bam file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4323 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java

@@ -113,7 +113,7 @@ public class StratifiedAlignmentContext<RBP extends ReadBackedPileup> {
                 contexts.put(sampleName,new StratifiedAlignmentContext<RBP>(loc,pileupBySample));
             else {
                 if(assumedSingleSample == null) {
-                    throw new UserException.MalformedBam(pileupBySample.iterator().next().getRead(), "Missing read group for read");
+                    throw new UserException.ReadMissingReadGroup(pileupBySample.iterator().next().getRead());
                 }
                 contexts.put(assumedSingleSample,new StratifiedAlignmentContext<RBP>(loc,pileupBySample));
             }

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

@@ -187,7 +187,7 @@ public class UnifiedGenotyperEngine {
             // annotate the call, if possible
             if ( call != null && call.vc != null && annotationEngine != null ) {
                 // first off, we want to use the *unfiltered* context for the annotations
-                stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(rawContext.getBasePileup());
+                stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE);
 
                 Collection<VariantContext> variantContexts = annotationEngine.annotateContext(tracker, refContext, stratifiedContexts, call.vc);
                 call.vc = variantContexts.iterator().next(); //We know the collection will always have exactly 1 element.

java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java

@@ -79,7 +79,8 @@ public class SequenceDictionaryUtils {
      * @param dict2 the sequence dictionary dict2
      */
     public static void validateDictionaries(Logger logger, String name1, SAMSequenceDictionary dict1, String name2, SAMSequenceDictionary dict2) {
-        switch ( compareDictionaries(dict1, dict2) ) {
+        SequenceDictionaryCompatability type = compareDictionaries(dict1, dict2);
+        switch ( type ) {
             case IDENTICAL:
                 return;
             case COMMON_SUBSET:
@@ -104,7 +105,7 @@ public class SequenceDictionaryUtils {
                 break;
             }
 
-            case NON_CANONICAL_HUMAN_ORDER:
+            case NON_CANONICAL_HUMAN_ORDER: {
                 UserException ex = new UserException.IncompatibleSequenceDictionaries("Human genome sequence provided in non-canonical ordering.  For safety's sake the GATK requires contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs",
                         name1, dict1, name2, dict2);
 
@@ -112,11 +113,17 @@ public class SequenceDictionaryUtils {
                     logger.warn(ex.getMessage());
                 else
                     throw ex;
+            }
 
-            case OUT_OF_ORDER:
+            case OUT_OF_ORDER: {
-                throw new UserException.IncompatibleSequenceDictionaries("Order of contigs differences, which is unsafe", name1, dict1, name2, dict2);
+                UserException ex = new UserException.IncompatibleSequenceDictionaries("Order of contigs differences, which is unsafe", name1, dict1, name2, dict2);
+                if ( allowNonFatalIncompabilities() )
+                    logger.warn(ex.getMessage());
+                else
+                    throw ex;
+            } break;
             default:
-                throw new ReviewedStingException("Unexpected SequenceDictionaryComparison type");
+                throw new ReviewedStingException("Unexpected SequenceDictionaryComparison type: " + type);
         }
     }
 

java/src/org/broadinstitute/sting/utils/exceptions/UserException.java

@@ -112,7 +112,7 @@ public class UserException extends ReviewedStingException {
 
     public static class MalformedBam extends UserException {
         public MalformedBam(SAMRecord read, String message) {
-            super(String.format("SAM/BAM file %s is malformed: %s", read.getFileSource(), message));
+            super(String.format("SAM/BAM file %s is malformed: %s", read.getFileSource().getReader(), message));
         }
     }
 
@@ -133,7 +133,7 @@ public class UserException extends ReviewedStingException {
 
         public MissortedBAM(SAMFileHeader.SortOrder order, SAMRecord read, String message) {
             super(String.format("Missorted Input SAM/BAM file %s: file sorted in %s order but %s is required; %s",
-                    read.getFileSource(), read.getHeader().getSortOrder(), order, message));
+                    read.getFileSource().getReader(), read.getHeader().getSortOrder(), order, message));
         }
 
         public MissortedBAM(String message) {