UnifiedGenotyper bugfix: don't create haplotypes with 0 bases

-- The PairHMM no longer allows us to create haplotypes with 0 bases.  The UG indel caller used to create such haplotypes.  Now we assign -Double.MAX_VALUE likelihoods to such haplotypes.
-- Add integration test to cover this case, along with private/testdata BAM
-- [Fixes #47523579]

protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java

@@ -388,20 +388,22 @@ public class PairHMMIndelErrorModel {
                             System.out.format("indStart: %d indStop: %d WinStart:%d WinStop:%d start: %d stop: %d readLength: %d C:%s\n",
                                     indStart, indStop, ref.getWindow().getStart(), ref.getWindow().getStop(), startLocationInRefForHaplotypes, stopLocationInRefForHaplotypes, read.getReadLength(), read.getCigar().toString());
 
-                        final byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
+                        final byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(), (int)indStart, (int)indStop);
-                                (int)indStart, (int)indStop);
 
-                        if (firstHap) {
+                        // it's possible that the indel starts at the last base of the haplotypes
-                            //no need to reallocate arrays for each new haplotype, as length won't change
+                        if ( haplotypeBases.length == 0 ) {
-                            pairHMM.initialize(readBases.length, haplotypeBases.length);
+                            readLikelihood = -Double.MAX_VALUE;
-                            firstHap = false;
+                        } else {
+                            if (firstHap) {
+                                //no need to reallocate arrays for each new haplotype, as length won't change
+                                pairHMM.initialize(readBases.length, haplotypeBases.length);
+                                firstHap = false;
+                            }
+
+                            readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals,
+                                    baseInsertionQualities, baseDeletionQualities, contextLogGapContinuationProbabilities, firstHap);
                         }
 
-
-                        readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals,
-                                baseInsertionQualities, baseDeletionQualities, contextLogGapContinuationProbabilities, firstHap);
-
-
                         if (DEBUG) {
                             System.out.println("H:"+new String(haplotypeBases));
                             System.out.println("R:"+new String(readBases));

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java

@@ -51,6 +51,7 @@ import org.testng.annotations.Test;
 
 import java.io.File;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
@@ -194,4 +195,14 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                 Arrays.asList("3f07efb768e08650a7ce333edd4f9a52"));
         executeTest("test minIndelFraction 1.0", spec);
     }
+
+    // No testing of MD5 here, we previously blew up due to a 0 length haplotypes, so we just need to pass
+    @Test
+    public void testHaplotype0Length() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T UnifiedGenotyper -I " + privateTestDir + "haplotype0.bam -L 20:47507681 -R " + b37KGReference + " -baq CALCULATE_AS_NECESSARY -glm BOTH -o /dev/null",
+                0,
+                Collections.<String>emptyList());
+        executeTest("testHaplotype0Length", spec);
+    }
 }