+
+ /**
+ * Get the list of chromosomes or contigs from the file (listed in SQ entries
+ * in BAM file header)
+ *
+ * @return array of chromosome/contig strings
+ */
+ @Override
+ public Object[] preprocess()
+ {
+ List<SAMSequenceRecord> refSeqs = fileReader.getFileHeader()
+ .getSequenceDictionary().getSequences();
+ List<String> chrs = new ArrayList<>();
+
+ for (SAMSequenceRecord ref : refSeqs)
+ {
+ chrs.add(ref.getSequenceName());
+ }
+ return chrs.toArray();
+ }
+
+ public void setOptions(String chr, int s, int e)
+ {
+ chromosome = chr;
+ start = s;
+ end = e;
+ }