Bug fix in assembly for edge case in which the extendPartialHaplotype function was filling in deletions in the middle of haplotypes.

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java

@@ -438,7 +438,8 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
         byte[] newHaplotypeBases = haplotype.getBases();
         int refPos = activeRegionStart;
         int hapPos = 0;
-        for( CigarElement ce : cigar.getCigarElements() ) {
+        for( int iii = 0; iii < cigar.getCigarElements().size(); iii++ ) {
+            final CigarElement ce = cigar.getCigarElement(iii);
             switch (ce.getOperator()) {
                 case M:
                     refPos += ce.getLength();
@@ -450,16 +451,17 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
                     newCigar.add(ce);
                     break;
                 case D:
-                    refPos += ce.getLength();
+                    if( iii == 0 || iii == cigar.getCigarElements().size() - 1 ) {
-                    newCigar.add(ce);
-                    break;
-                case X:
                         newHaplotypeBases = ArrayUtils.addAll( Arrays.copyOfRange(newHaplotypeBases, 0, hapPos),
                                 ArrayUtils.addAll(Arrays.copyOfRange(refWithPadding, refPos, refPos + ce.getLength()),
                                 Arrays.copyOfRange(newHaplotypeBases, hapPos, newHaplotypeBases.length)));
-                    refPos += ce.getLength();
                         hapPos += ce.getLength();
+                        refPos += ce.getLength();
                         newCigar.add(new CigarElement(ce.getLength(), CigarOperator.M));
+                    } else {
+                        refPos += ce.getLength();
+                        newCigar.add(ce);
+                    }
                     break;
                 default:
                     throw new IllegalStateException("Unsupported cigar operator detected: " + ce.getOperator());

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java

@@ -310,31 +310,13 @@ public class KBestPaths {
             if( swCigar.numCigarElements() > 6 ) { // this bubble is too divergent from the reference
                 returnCigar.add(new CigarElement(1, CigarOperator.N));
             } else {
-                int skipElement = -1;
-                if( fromVertex == null ) {
-                    for( int iii = 0; iii < swCigar.numCigarElements(); iii++ ) {
-                        final CigarElement ce = swCigar.getCigarElement(iii);
-                        if( ce.getOperator().equals(CigarOperator.D) ) {
-                            skipElement = iii;
-                            break;
-                        }
-                    }
-                } else if (toVertex == null ) {
-                    for( int iii = swCigar.numCigarElements() - 1; iii >= 0; iii-- ) {
-                        final CigarElement ce = swCigar.getCigarElement(iii);
-                        if( ce.getOperator().equals(CigarOperator.D) ) {
-                            skipElement = iii;
-                            break;
-                        }
-                    }
-                }
                 for( int iii = 0; iii < swCigar.numCigarElements(); iii++ ) {
                     // now we need to remove the padding from the cigar string
                     int length = swCigar.getCigarElement(iii).getLength();
                     if( iii == 0 ) { length -= padding.length; }
                     if( iii == swCigar.numCigarElements() - 1 ) { length -= padding.length; }
                     if( length > 0 ) {
-                        returnCigar.add(new CigarElement(length, (skipElement == iii ? CigarOperator.X : swCigar.getCigarElement(iii).getOperator())));
+                        returnCigar.add(new CigarElement(length, swCigar.getCigarElement(iii).getOperator()));
                     }
                 }
                 if( (refBytes == null && returnCigar.getReferenceLength() != 0) || ( refBytes != null && returnCigar.getReferenceLength() != refBytes.length ) ) {

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java

@@ -87,12 +87,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleGGAComplex() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
-                "417174e043dbb8b86cc3871da9b50536");
+                "fd3412030628fccf77effdb1ec03dce7");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
-                "9563e3c1eee2ef46afc7822af0bb58a8");
+                "633e8930a263e34def5e097889dd9805");
     }
 }

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -69,12 +69,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSample() {
-        HCTest(CEUTRIO_BAM, "", "4a2880f0753e6e813b9e0c35209b3708");
+        HCTest(CEUTRIO_BAM, "", "694d6ea7f0f305854d4108379d68de75");
     }
 
     @Test
     public void testHaplotypeCallerSingleSample() {
-        HCTest(NA12878_BAM, "", "b3bffabb7aafd43e0339958395e6aa10");
+        HCTest(NA12878_BAM, "", "995501d8af646af3b6eaa4109e2fb4a0");
     }
 
     @Test(enabled = false) // can't annotate the rsID's yet
@@ -85,7 +85,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
-                "fa1b92373c89d2238542a319ad25c257");
+                "627124af27dc4556d83df1a04e4b9f97");
     }
 
     private void HCTestIndelQualityScores(String bam, String args, String md5) {
@@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerSingleSampleIndelQualityScores() {
-        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "852623c93feef5e62fcb555beedc8c53");
+        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "205fc8647b908c0dab7b5c6d6b78c0c2");
     }
 
     @Test
@@ -118,7 +118,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestStructuralIndels() {
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("9296f1af6cf1f1cc4b79494eb366e976"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("f1250a8ecd404443dcca20741a74ec4f"));
         executeTest("HCTestStructuralIndels: ", spec);
     }
 
@@ -148,7 +148,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void testReducedBamWithReadsNotFullySpanningDeletion() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
-                Arrays.asList("addceb63f5bfa9f11e15335d5bf641e9"));
+                Arrays.asList("d3eb900eecdafafda3170f67adff42ae"));
         executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
     }
 }