Merge branch 'master' of github.com:broadinstitute/gsa-unstable

protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java

@@ -46,7 +46,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import com.sun.org.apache.bcel.internal.generic.AALOAD;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -60,7 +59,6 @@ import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.variant.variantcontext.Genotype;
 import org.broadinstitute.variant.variantcontext.GenotypesContext;
 import org.broadinstitute.variant.variantcontext.VariantContext;
-import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.Arrays;
 import java.util.HashMap;
@@ -68,7 +66,7 @@ import java.util.List;
 import java.util.Map;
 
 /**
- * Variant confidence (from the QUAL field) / unfiltered depth.
+ * Variant confidence (from the QUAL field) / unfiltered depth of non-reference samples.  Note that the QD is also normalized by event length.
  *
  * Low scores are indicative of false positive calls and artifacts.  Note that QualByDepth requires sequencing
  * reads associated with the samples with polymorphic genotypes.

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java

@@ -50,6 +50,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.sam.AlignmentStartWithNoTiesComparator;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
+import java.util.Collections;
 import java.util.Set;
 import java.util.TreeSet;
 
@@ -126,7 +127,7 @@ public class SingleSampleCompressor {
     }
 
     public Set<GATKSAMRecord> closeVariantRegions(CompressionStash regions) {
-        return slidingWindow.closeVariantRegions(regions);
+        return slidingWindow == null ? Collections.<GATKSAMRecord>emptySet() : slidingWindow.closeVariantRegions(regions);
     }
 
 }

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java

@@ -682,7 +682,7 @@ public class SlidingWindow {
             int windowHeaderStart = getStartLocation(windowHeader);
 
             for (SimpleGenomeLoc region : regions) {
-                if (region.isFinished() && region.getContig() == contig && region.getStart() >= windowHeaderStart && region.getStop() <= windowHeaderStart + windowHeader.size()) {
+                if (region.isFinished() && region.getContig() == contig && region.getStart() >= windowHeaderStart && region.getStop() < windowHeaderStart + windowHeader.size()) {
                     int start = region.getStart() - windowHeaderStart;
                     int stop = region.getStop() - windowHeaderStart;
 

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala

@@ -21,3 +21,33 @@
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.queue.qscripts.examples
+
+import org.broadinstitute.sting.queue.function.RetryMemoryLimit
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.queue.extensions.gatk._
+
+class ExampleRetryMemoryLimit extends QScript {
+  @Input(doc="The reference file for the bam files.", shortName="R")
+  var referenceFile: File = _
+
+  @Input(doc="Bam file to genotype.", shortName="I")
+  var bamFile: File = _
+
+  def script() {
+    for (scatterCount <- 1 to 2) {
+      val ug = new UnifiedGenotyper with RetryMemoryLimit
+      // First run with 1m
+      ug.memoryLimit = .001
+      // On retry run with 1g
+      ug.retryMemoryFunction = (d => d * 1000)
+      ug.reference_sequence = referenceFile
+      ug.input_file = Seq(bamFile)
+      ug.out = swapExt(bamFile, ".bam", ".scattered_%d.vcf".format(scatterCount))
+      ug.scatterCount = scatterCount
+      add(ug)
+    }
+  }
+}