Beispiel #1
0
 /**
  * Gets the GATK samples database
  *
  * @link GenomeAnalysisEngine.getSampleDB
  * @return the GATK samples database or null if no genome analysis toolkit.
  */
 public SampleDB getSampleDB() {
   if (toolkit == null) return null;
   else return toolkit.getSampleDB();
 }
Beispiel #2
0
 /**
  * Gets the master sequence dictionary for this walker
  *
  * @link GenomeAnalysisEngine.getMasterSequenceDictionary
  * @return the master sequence dictionary or null if no genome analysis toolkit.
  */
 protected SAMSequenceDictionary getMasterSequenceDictionary() {
   if (toolkit == null) return null;
   else return toolkit.getMasterSequenceDictionary();
 }
Beispiel #3
0
 /**
  * Gets the GATK argument collection
  *
  * @link GenomeAnalysisEngine.getArguments
  * @return the GATK argument collection or null if no genome analysis toolkit.
  */
 public GATKArgumentCollection getArguments() {
   if (toolkit == null) return null;
   else return toolkit.getArguments();
 }