From ccae6a5b9264350050695de05dad098884ea99f9 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 22 Oct 2012 11:48:34 -0400 Subject: [PATCH] Fixed the RR bug I (knowingly) introduced last week: turns out we can't trust a context size's worth of data from the previous marking. I think Mauricio warned me about this but I forgot. --- .../gatk/walkers/compression/reducereads/SlidingWindow.java | 5 ++++- 1 file changed, 4 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 63524ae82..32abe8ef6 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 @@ -276,7 +276,10 @@ public class SlidingWindow { final int windowHeaderStartLocation = getStartLocation(windowHeader); final int sizeOfMarkedRegion = stop - windowHeaderStartLocation + contextSize + 1; - final int lastPositionMarked = markedSites.updateRegion(windowHeaderStartLocation, sizeOfMarkedRegion); + + // copy over as many bits as we can from the previous calculation. Note that we can't trust the + // last (contextSize - 1) worth of bits because we may not have actually looked at variant regions there. + final int lastPositionMarked = markedSites.updateRegion(windowHeaderStartLocation, sizeOfMarkedRegion) - contextSize - 1; final int locationToProcess = Math.min(lastPositionMarked, stop - contextSize); // update the iterator to the correct position