From 32e5dceef98bcb5a2bf724869005410867086ec2 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Mon, 22 Feb 2010 19:27:31 +0000 Subject: [PATCH] Moving comments. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2865 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/recalibration/TableRecalibrationWalker.java | 2 +- .../gatk/walkers/variantoptimizer/AnnotationDataManager.java | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java index 7cfd069e5..0a5b1c71d 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java @@ -50,7 +50,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * conditions: * * The above copyright notice and this permission notice shall be - + * included in all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java index d8c18db32..64d2420d1 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java @@ -130,7 +130,8 @@ public class AnnotationDataManager { // else, continue accumulating variants because this bin isn't full yet } - if( thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) != 0 ) { // One final bin that may not have been dumped out + // One final bin that may not have been dumped out + if( thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) != 0 ) { output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.FULL_SET ) + "\t" + thisAnnotationBin.calcDBsnpRate() + "\t" + thisAnnotationBin.calcTPrate() + "\t" + thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) + "\tall"); output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.NOVEL_SET ) + "\t-1\t-1\t" + thisAnnotationBin.numVariants( AnnotationDatum.NOVEL_SET ) + "\tnovel");