public void setupTest2(
final int ID,
final String readGroupId,
final SAMReadGroupRecord readGroupRecord,
final String sample,
final String library,
final SAMFileHeader header,
final SAMRecordSetBuilder setBuilder)
throws IOException {
final String separator = ":";
final int contig1 = 0;
final int contig2 = 1;
final int contig3 = 2;
readGroupRecord.setSample(sample);
readGroupRecord.setPlatform(platform);
readGroupRecord.setLibrary(library);
readGroupRecord.setPlatformUnit(readGroupId);
setBuilder.setReadGroup(readGroupRecord);
setBuilder.setUseNmFlag(true);
setBuilder.setHeader(header);
final int max = 800;
final int min = 1;
final Random rg = new Random(5);
// add records that align to all 3 chr in reference file
for (int i = 0; i < NUM_READS; i++) {
final int start = rg.nextInt(max) + min;
final String newReadName = READ_NAME + separator + ID + separator + i;
if (i <= NUM_READS / 3) {
setBuilder.addPair(newReadName, contig1, start + ID, start + ID + LENGTH);
} else if (i < (NUM_READS - (NUM_READS / 3))) {
setBuilder.addPair(newReadName, contig2, start + ID, start + ID + LENGTH);
} else {
setBuilder.addPair(newReadName, contig3, start + ID, start + ID + LENGTH);
}
}
}
