From 6c9f86bb4dba2ecbb5cb8ad5949329c7191652a3 Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 11 Nov 2009 18:37:36 +0000 Subject: [PATCH] Removed unnecessary output and added debugging print() routine git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2020 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/filters/RatioFilter.java | 6 +++--- .../broadinstitute/sting/utils/genotype/vcf/VCFRecord.java | 7 +++++++ 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java index 3f923401a..463bdaf64 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java @@ -71,9 +71,9 @@ public abstract class RatioFilter implements VariantExclusionCriterion { // int n = counts.first + counts.second; double value = counts.first / (1.0 * counts.first + counts.second); - logger.info(String.format("%s: counts1=%d (%.2f), counts2=%d (%.2f), n=%d, value=%f, exclude=%b, location=%s, bases=%s", - name, counts.first, counts.first / (0.01 * n), counts.second, counts.second / (0.01 * n), n, - value, exclude, variant.getLocation(), pileup.getBases())); + //logger.info(String.format("%s: counts1=%d (%.2f), counts2=%d (%.2f), n=%d, value=%f, exclude=%b, location=%s, bases=%s", + // name, counts.first, counts.first / (0.01 * n), counts.second, counts.second / (0.01 * n), n, + // value, exclude, variant.getLocation(), pileup.getBases())); } // TODO - this calculation needs to be parameterized correctly diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java index df9675f89..4f4bb7bd3 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java @@ -334,9 +334,16 @@ public class VCFRecord { * @param value it's value as a string */ public void addInfoField(String key, String value) { + //System.out.printf("Adding info field %s=%s%n", key, value); this.mInfoFields.put(key, value); } + public void printInfoFields() { + for ( Map.Entry e : this.mInfoFields.entrySet() ) { + System.out.printf(" Current info field %s=%s this=%s%n", e.getKey(), e.getValue(), this); + } + } + /** * add an info field to the record