From ac3627145744cb2a9e9a384063beaeea78251554 Mon Sep 17 00:00:00 2001 From: Roger Zurawicki Date: Tue, 23 Aug 2011 11:26:00 -0400 Subject: [PATCH] Fixed extra reads showing up in Variable Sites Reads that were not hard clipped for the variable site no longer show up in output file Walker now uses unclippedStart of Read to determine position in the sliding Window --- .../org/broadinstitute/sting/utils/clipreads/ReadClipper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java index 6248849f9..44b77533f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java @@ -54,7 +54,7 @@ public class ReadClipper { int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart); int stop = (refStop < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop); - System.out.println("Clipping start/stop: " + start + "/" + stop); + //System.out.println("Clipping start/stop: " + start + "/" + stop); this.addOp(new ClippingOp(start, stop)); return clipRead(ClippingRepresentation.HARDCLIP_BASES); }