throw new Exception("RANGES and RANGE were both specified.\n");
}
else if(null == RANGES && null == RANGE) {
this.inputRanges = new Ranges(this.referenceDictionary);
this.outputRanges = new Ranges(this.referenceDictionary);
this.io = new SAMRecordIO(INPUT, OUTPUT, PROGRAM_VERSION, false, this.referenceDictionary);
}
else {
if(null != RANGES) {
IoUtil.assertFileIsReadable(RANGES);
this.inputRanges = new Ranges(RANGES, this.referenceDictionary, OFFSET);
this.outputRanges = new Ranges(RANGES, this.referenceDictionary, 0);
}
else {
this.inputRanges = new Ranges(RANGE, this.referenceDictionary, OFFSET);
this.outputRanges = new Ranges(RANGE, this.referenceDictionary, 0);
}
this.io = new SAMRecordIO(INPUT, OUTPUT, PROGRAM_VERSION, true, this.referenceDictionary);
}
this.inputRangesIterator = this.inputRanges.iterator();
this.outputRangesIterator = this.outputRanges.iterator();
if(!this.inputRangesIterator.hasNext()) {