Merge pull request #1451 from broadinstitute/sl_issue_1345_fix_2

Changed maximum allowed GQB value to 100.

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java

@@ -366,12 +366,17 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
      * sites are compressed into bands of similar genotype quality (GQ) that are emitted as a single VCF record. See
      * the FAQ documentation for more details about the GVCF format.
      *
-     * This argument allows you to set the GQ boundaries. HC expects a list of multiple GQ threshold values. To pass
+     * This argument allows you to set the GQ bands. HC expects a list of strictly increasing GQ values
-     * multiple values, you provide them one by one with the argument, as in `-GQB 10 -GQB 20 -GQB 30` and so on. Note
+     * that will act as exclusive upper bounds for the GQ bands. To pass multiple values,
-     * that GQ values are capped at 99 in the GATK, so values must be integers in [1, 99].
+     * you provide them one by one with the argument, as in `-GQB 10 -GQB 20 -GQB 30` and so on
+     * (this would set the GQ bands to be `[0, 10), [10, 20), [20, 30)` and so on, for example).
+     * Note that GQ values are capped at 99 in the GATK, so values must be integers in [1, 100].
+     * If the last value is strictly less than 100, the last GQ band will start at that value (inclusive)
+     * and end at 100 (exclusive).
      */
     @Advanced
-    @Argument(fullName="GVCFGQBands", shortName="GQB", doc="GQ thresholds for reference confidence bands (must be in [1, 99] and specified in increasing order)", required = false)
+    @Argument(fullName="GVCFGQBands", shortName="GQB", doc="Exclusive upper bounds for reference confidence GQ bands " +
+            "(must be in [1, 100] and specified in increasing order)", required = false)
     protected List<Integer> GVCFGQBands = new ArrayList<Integer>(70) {{
         for (int i=1; i<=60; ++i) add(i);
         add(70); add(80); add(90); add(99);

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java

@@ -98,20 +98,34 @@ public class GVCFWriter implements VariantContextWriter {
      * @return a non-null string if something is wrong (string explains issue)
      */
     protected static List<HomRefBlock> parsePartitions(final List<Integer> GQPartitions, final int defaultPloidy) {
-        if ( GQPartitions == null ) throw new IllegalArgumentException("The list of GQ partitions cannot be null.");
+        if ( GQPartitions == null ) {
-        if ( GQPartitions.isEmpty() ) throw new IllegalArgumentException("The list of GQ partitions cannot be empty.");
+            throw new IllegalArgumentException("The list of GQ partitions cannot be null.");
+        }
+        if ( GQPartitions.isEmpty() ) {
+            throw new IllegalArgumentException("The list of GQ partitions cannot be empty.");
+        }
 
         final List<HomRefBlock> result = new LinkedList<>();
         int lastThreshold = 0;
         for ( final Integer value : GQPartitions ) {
-            if ( value == null || value <= 0 ) throw new IllegalArgumentException("The list of GQ partitions contains a null or non-positive integer.");
+            if ( value == null || value <= 0 ) {
-            if ( value < lastThreshold ) throw new IllegalArgumentException(String.format("The list of GQ partitions is out of order. Previous value is %d but the next is %d.", lastThreshold, value));
+                throw new IllegalArgumentException("The list of GQ partitions contains a null or non-positive integer.");
-            if ( value == lastThreshold ) throw new IllegalArgumentException(String.format("The value %d appears more than once in the list of GQ partitions.", value));
+            }
-            if ( value > MAX_GENOTYPE_QUAL ) throw new IllegalArgumentException(String.format("The value %d in the list of GQ partitions is greater than VCFConstants.MAX_GENOTYPE_QUAL = %d.", value, VCFConstants.MAX_GENOTYPE_QUAL));
+            if ( value < lastThreshold ) {
+                throw new IllegalArgumentException(String.format("The list of GQ partitions is out of order. " +
+                        "Previous value is %d but the next is %d.", lastThreshold, value));
+            }
+            if ( value == lastThreshold ) {
+                throw new IllegalArgumentException(String.format("The value %d appears more than once in the list of GQ partitions.", value));
+            }
+            if ( value > MAX_GENOTYPE_QUAL + 1 ) {
+                throw new IllegalArgumentException(String.format("The value %d in the list of GQ partitions is " +
+                        "greater than VCFConstants.MAX_GENOTYPE_QUAL + 1 = %d.", value, VCFConstants.MAX_GENOTYPE_QUAL + 1));
+            }
             result.add(new HomRefBlock(lastThreshold, value, defaultPloidy));
             lastThreshold = value;
         }
-        if (lastThreshold <= MAX_GENOTYPE_QUAL ) {
+        if ( lastThreshold <= MAX_GENOTYPE_QUAL ) {
             result.add(new HomRefBlock(lastThreshold, MAX_GENOTYPE_QUAL + 1, defaultPloidy));
         }
         return result;

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java

@@ -441,7 +441,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
                 {Arrays.asList(-1, 10, 20)},
                 {Arrays.asList(10, 20, 1)},
                 {Arrays.asList(10, 10, 20)},
-                {Arrays.asList(10, 20, VCFConstants.MAX_GENOTYPE_QUAL + 1)}
+                {Arrays.asList(10, 20, VCFConstants.MAX_GENOTYPE_QUAL + 2)}
         };
     }
     @Test(dataProvider = "dataBadGQBValues")

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java

@@ -390,7 +390,9 @@ public class GVCFWriterUnitTest extends BaseTest {
         tests.add(new Object[]{Arrays.asList(1, 1, 10), false, null});
         tests.add(new Object[]{Arrays.asList(1, 10, VCFConstants.MAX_GENOTYPE_QUAL - 1), true, Arrays.asList(0, 1, 10, VCFConstants.MAX_GENOTYPE_QUAL - 1)});
         tests.add(new Object[]{Arrays.asList(1, 10, VCFConstants.MAX_GENOTYPE_QUAL), true, Arrays.asList(0, 1, 10, VCFConstants.MAX_GENOTYPE_QUAL)});
-        tests.add(new Object[]{Arrays.asList(1, 10, VCFConstants.MAX_GENOTYPE_QUAL + 1), false, null});
+        tests.add(new Object[]{Arrays.asList(1, 10, VCFConstants.MAX_GENOTYPE_QUAL + 1), true, Arrays.asList(0, 1, 10)});
+        tests.add(new Object[]{Collections.singletonList(VCFConstants.MAX_GENOTYPE_QUAL + 1), true, Collections.singletonList(0)});
+        tests.add(new Object[]{Arrays.asList(1, 10, VCFConstants.MAX_GENOTYPE_QUAL + 2), false, null});
 
         return tests.toArray(new Object[][]{});
     }