@BeforeTest
public void setUp() {
builder.setReadLength(READ_LENGTH);
// Will be kept when an interval overlaps chromosome 1 in the first 151
// bases.
builder.addPair("mapped_pair_chr1", 0, 1, 151);
// Will be kept when an interval overlaps chromsome 2 in the first 151
// bases.
builder.addPair("mapped_pair_chr2", 1, 1, 151);
// The first read should pass and second should not, but both will
// be kept in first test.
builder.addPair("one_of_pair", 0, 1, 1000);
// The second read is unmapped, but both should be kept in an
// interval test where the interval includes chromosome four, where
// read one will overlap.
builder.addPair(
"second_mate_unmapped",
3,
-1,
1,
1000,
false,
true,
"151M",
null,
false,
false,
false,
false,
-1);
// The first read is unmapped but both should be kept in an
// interval test where the interval includes chromosome four, where
// read two will overlap.
builder.addPair(
"first_mate_unmapped",
-1,
3,
1000,
1,
true,
false,
null,
"151M",
false,
false,
false,
false,
-1);
// This pair will overlap any interval that includes chromosome 1:1000
builder.addPair("prove_one_of_pair", 0, 1000, 1000);
// These reads are unmapped and will not map to any intervals, so they
// are never kept. This is tested below.
builder.addPair(
"both_unmapped", -1, -1, 1, 1, true, true, null, null, false, false, false, false, -1);
// Secondary alignments are never kept by the interval filter.
builder.addFrag("mapped_pair_chr1", 0, 1, false, false, "151M", null, -1, true, false);
// Supplementary alignment are never kept by the interval filter.
builder.addFrag("mapped_pair_chr1", 0, 1, false, false, "151M", null, -1, false, true);
}
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);
}
}
}
