From 876e40466a43660d9fbf280bb03a3436b29e20f0 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 26 Jun 2013 14:48:09 -0400
Subject: [PATCH] Proper fix for previous RR -cancer_mode fix.

I "fixed" this once before but instead of testing with unit tests I used integration tests.
Bad decision.

The proper fix is in now, with a bonafide unit test included.
---
 .../reducereads/SlidingWindow.java            |  2 +-
 .../reducereads/SlidingWindowUnitTest.java    | 27 +++++++++++++++++++
 2 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
index 0425af3df..5115a6777 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
@@ -878,7 +878,7 @@ public class SlidingWindow {
                     int stop = region.getStop() - windowHeaderStart;
 
                     // make sure the bitset is complete given the region (it might not be in multi-sample mode)
-                    if ( region.getStop() > markedSites.getStartLocation() + markedSites.getVariantSiteBitSet().length )
+                    if ( region.getStop() > markedSites.getStartLocation() + markedSites.getVariantSiteBitSet().length - 1 )
                         markSites(region.getStop());
 
                     CloseVariantRegionResult closeVariantRegionResult = closeVariantRegion(start, stop, knownSnpPositions);
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
index bf45fc298..bd0a8933c 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
@@ -253,6 +253,33 @@ public class SlidingWindowUnitTest extends BaseTest {
         return count;
     }
 
+    @Test(enabled = true)
+    public void testMarkingRegionInCancerMode() {
+
+        final int contextSize = 10;
+        final SlidingWindow slidingWindow = new SlidingWindow("1", 0, contextSize, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 0.05, 20, 20, 100, ReduceReads.DownsampleStrategy.Normal, false);
+        slidingWindow.addRead(createSimpleRead("1", 0, 34, 75));
+        slidingWindow.addRead(createSimpleRead("2", 0, 97, 73));
+        slidingWindow.addRead(createSimpleRead("3", 0, 98, 75));
+        slidingWindow.addRead(createSimpleRead("4", 0, 98, 75));
+        slidingWindow.addRead(createSimpleRead("5", 0, 98, 75));
+
+        final CompressionStash regions = new CompressionStash();
+        regions.add(new FinishedGenomeLoc("1", 0, 89, 109, true));
+
+        slidingWindow.closeVariantRegions(regions, null, false);
+        Assert.assertEquals(slidingWindow.getMarkedSitesForTesting().getVariantSiteBitSet().length, 76 + contextSize);
+    }
+
+    private GATKSAMRecord createSimpleRead(final String name, final int refIndex, final int alignmentStart, final int length) {
+
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, name, refIndex, alignmentStart, length);
+        read.setReadBases(Utils.dupBytes((byte) 'A', length));
+        read.setBaseQualities(Utils.dupBytes((byte) 30, length));
+        read.setMappingQuality(60);
+        return read;
+    }
+
 
     /////////////////////////////////////////////////////////////////
     //// This section tests the consensus creation functionality ////