/**
* outputFeatureInVCF.
*
* @param buffer a {@link java.lang.StringBuffer} object.
* @param feature a {@link com.github.seqware.queryengine.model.Feature} object.
* @return a boolean.
*/
public static boolean outputFeatureInVCF(StringBuffer buffer, Feature feature) {
boolean caughtNonVCF = false;
buffer.append(feature.getSeqid()).append("\t").append(feature.getStart() + 1).append("\t");
if (feature.getTagByKey(VCF, ImportConstants.VCF_SECOND_ID) == null) {
buffer.append(".\t");
} else {
buffer
.append(feature.getTagByKey(VCF, ImportConstants.VCF_SECOND_ID).getValue().toString())
.append("\t");
}
try {
buffer
.append(
feature.getTagByKey(VCF, ImportConstants.VCF_REFERENCE_BASE).getValue().toString())
.append("\t");
buffer
.append(feature.getTagByKey(VCF, ImportConstants.VCF_CALLED_BASE).getValue().toString())
.append("\t");
buffer.append(feature.getScore() == null ? "." : feature.getScore()).append("\t");
buffer
.append(feature.getTagByKey(VCF, ImportConstants.VCF_FILTER).getValue().toString())
.append("\t");
buffer.append(feature.getTagByKey(VCF, ImportConstants.VCF_INFO).getValue().toString());
} catch (NullPointerException npe) {
if (!caughtNonVCF) {
Logger.getLogger(VCFDumper.class.getName()).info("VCF exporting non-VCF feature");
}
// this may occur when exporting Features that were not originally VCF files
caughtNonVCF = true;
}
return caughtNonVCF;
}