// NB: this test should return different results than MarkDuplicatesWithMateCigar
@Test
public void testTwoMappedPairsWithSoftClippingFirstOfPairOnly() {
final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester();
// NB: no duplicates
// 5'1: 2, 5'2:46+73M=118
// 5'1: 2, 5'2:51+68M=118
tester.addMappedPair(
0, 12, 46, false, false, "6S42M28S", "3S73M", true, 50); // only add the first one
// NB: this next record should not be a duplicate in MarkDuplicates
tester.addMappedPair(
0, 12, 51, false, false, "6S42M28S", "8S68M", true, 50); // only add the first one
tester.runTest();
}
@Test
public void testWithBarcodeDuplicate() {
final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester();
tester.addMatePair(
"RUNID:1:1:15993:13361",
2,
41212324,
41212310,
false,
false,
false,
false,
"33S35M",
"19S49M",
true,
true,
false,
false,
false,
DEFAULT_BASE_QUALITY);
tester.addMatePair(
"RUNID:2:2:15993:13362",
2,
41212324,
41212310,
false,
false,
true,
true,
"33S35M",
"19S49M",
true,
true,
false,
false,
false,
DEFAULT_BASE_QUALITY);
final String barcodeTag = "BC";
for (final SAMRecord record : new IterableAdapter<SAMRecord>(tester.getRecordIterator())) {
record.setAttribute(barcodeTag, "Barcode1");
}
tester.addArg("BARCODE_TAG=" + barcodeTag);
tester.runTest();
}
@Test
public void testWithIndividualReadBarcodes() {
final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester();
final String readNameOne = "RUNID:1:1:15993:13361";
final String readNameTwo = "RUNID:2:2:15993:13362";
final String readNameThree = "RUNID:3:3:15993:13362";
// first two reads have the same barcode (all three), third read has a different barcode for the
// second end
tester.addMatePair(
readNameOne,
2,
41212324,
41212310,
false,
false,
false,
false,
"33S35M",
"19S49M",
true,
true,
false,
false,
false,
DEFAULT_BASE_QUALITY);
tester.addMatePair(
readNameTwo,
2,
41212324,
41212310,
false,
false,
true,
true,
"33S35M",
"19S49M",
true,
true,
false,
false,
false,
DEFAULT_BASE_QUALITY); // same barcode as the first
tester.addMatePair(
readNameThree,
2,
41212324,
41212310,
false,
false,
false,
false,
"33S35M",
"19S49M",
true,
true,
false,
false,
false,
DEFAULT_BASE_QUALITY);
final String barcodeTag = "BC";
final String readOneBarcodeTag =
"BX"; // want the same tag as the second end, since this is allowed
final String readTwoBarcodeTag = "BX";
for (final SAMRecord record : new IterableAdapter<SAMRecord>(tester.getRecordIterator())) {
record.setAttribute(barcodeTag, "Barcode1"); // same barcode
if (record.getFirstOfPairFlag()) { // always the same value for the first end
record.setAttribute(readOneBarcodeTag, "readOne1");
} else { // second end
if (record.getReadName().equals(readNameOne) || record.getReadName().equals(readNameTwo)) {
record.setAttribute(readTwoBarcodeTag, "readTwo1");
} else if (record.getReadName().equals(readNameThree)) {
record.setAttribute(readTwoBarcodeTag, "readTwo2");
}
}
}
tester.addArg("BARCODE_TAG=" + barcodeTag);
tester.addArg("READ_ONE_BARCODE_TAG=" + readOneBarcodeTag);
tester.addArg("READ_TWO_BARCODE_TAG=" + readTwoBarcodeTag);
tester.runTest();
}
@Test
public void testWithBarcodeComplex() {
final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester();
final String readNameOne = "RUNID:1:1:15993:13361";
final String readNameTwo = "RUNID:2:2:15993:13362";
final String readNameThree = "RUNID:3:3:15993:13362";
// first two reads have the same barcode, third read has a different barcode
tester.addMatePair(
readNameOne,
2,
41212324,
41212310,
false,
false,
false,
false,
"33S35M",
"19S49M",
true,
true,
false,
false,
false,
DEFAULT_BASE_QUALITY);
tester.addMatePair(
readNameTwo,
2,
41212324,
41212310,
false,
false,
true,
true,
"33S35M",
"19S49M",
true,
true,
false,
false,
false,
DEFAULT_BASE_QUALITY); // same barcode as the first
tester.addMatePair(
readNameThree,
2,
41212324,
41212310,
false,
false,
false,
false,
"33S35M",
"19S49M",
true,
true,
false,
false,
false,
DEFAULT_BASE_QUALITY);
final String barcodeTag = "BC";
for (final SAMRecord record : new IterableAdapter<SAMRecord>(tester.getRecordIterator())) {
if (record.getReadName().equals(readNameOne) || record.getReadName().equals(readNameTwo)) {
record.setAttribute(barcodeTag, "Barcode1");
} else if (record.getReadName().equals(readNameThree)) {
record.setAttribute(barcodeTag, "Barcode2");
}
}
tester.addArg("BARCODE_TAG=" + barcodeTag);
tester.runTest();
}
