Java Alignment Examples

Example #1

File: UnsplicedReadFilter.java Project: shaked-afik/scriptureV2

 @Override
 public boolean evaluate(Alignment align) {
   // if has splice junctions --> return false
   if (!align.getSpliceConnections().isEmpty()) {
     return false;
   }
   return true;
 }

Example #2

File: MappingQualityFilter.java Project: shaked-afik/scriptureV2

 @Override
 public boolean evaluate(Alignment align) {
   return ((align.isPaired() && align.getMappingQuality() >= minPairedEndQuality)
       || (!align.isPaired() && align.getMappingQuality() >= minSingleEndQuality));
 }