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oops, missing file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2009 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-11-10 13:25:18 +00:00
parent d316cbad4c
commit 7e30fe230a
1 changed files with 20 additions and 5 deletions
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25
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
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@ -220,17 +220,21 @@ public class VCFRecord {
} }
public boolean isFiltered() { public boolean isFiltered() {
String[] codes = getFilteringCodes(); String[] codes = getFilteringCodes();
if ( codes.length > 1 ) return true; if ( codes.length > 1 ) return true;
else if ( codes[0].equals(".") || codes[0].equals("0") ) return false; else if ( codes[0].equals(".") || codes[0].equals("0") ) return false;
else return true; else return true;
} }
public boolean hasFilteringCodes() { public boolean hasFilteringCodes() {
// todo --- currently always returns true // todo --- currently always returns true
return getFilteringCodes() != null; return getFilteringCodes() != null;
} }
public String getFilterString() {
return mFilterString;
}
/** /**
* get the information key-value pairs as a Map<> * get the information key-value pairs as a Map<>
* *
@ -333,6 +337,17 @@ public class VCFRecord {
this.mInfoFields.put(key, value); this.mInfoFields.put(key, value);
} }
/**
* add an info field to the record
*
* @param m A map from info keys to info values
*/
public void addInfoFields(Map<String,String> m) {
for ( Map.Entry<String, String> e : m.entrySet() )
addInfoField(e.getKey(), e.getValue());
}
/** /**
* the generation of a string representation, which is used by the VCF writer * the generation of a string representation, which is used by the VCF writer
* *