Esempio n. 1
0
 /**
  * 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;
 }