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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
This commit is contained in:
depristo 2009-11-11 18:37:36 +00:00
parent 637f02f392
commit 6c9f86bb4d
2 changed files with 10 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java
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@ -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

7
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
View File

@ -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<String, String> 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