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Moving comments. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2865 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-02-22 19:27:31 +00:00
parent b236714c8a
commit 32e5dceef9
2 changed files with 3 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -50,7 +50,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* conditions: * conditions:
* *
* The above copyright notice and this permission notice shall be * 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, * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
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@ -130,7 +130,8 @@ public class AnnotationDataManager {
// else, continue accumulating variants because this bin isn't full yet // 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() + output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.FULL_SET ) + "\t" + thisAnnotationBin.calcDBsnpRate() + "\t" + thisAnnotationBin.calcTPrate() +
"\t" + thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) + "\tall"); "\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"); output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.NOVEL_SET ) + "\t-1\t-1\t" + thisAnnotationBin.numVariants( AnnotationDatum.NOVEL_SET ) + "\tnovel");