/**
* Trims and splits complex calls.
*
* @param params params to check options
* @param original call to be trimmed and split (may be returned as the answer)
* @param denovoCorrector method for correcting de novo flags
* @return a list of calls. There can be more than one if the call can be split into separate
* calls that line up.
*/
public static List<Variant> trimSplit(
VariantParams params, Variant original, DenovoChecker denovoCorrector) {
if (params.callLevel() == VariantOutputLevel.ALL) {
return Collections.singletonList(original);
} else if (params.ionTorrent()) {
return Collections.singletonList(trim(original));
}
return split(trim(original), denovoCorrector);
}
public void testBad() {
Diagnostic.setLogStream();
final SAMRecord rec = new SAMRecord(new SAMFileHeader());
rec.setReadString("TATTAGGATTGAGACTGGTAAAATGGNCCACCAAG");
rec.setBaseQualityString("/725361840-525251.68,0,.52!222254/2");
final VariantParams params = VariantParams.builder().create();
try {
new AlignmentEnvironmentCG(
new VariantAlignmentRecord(rec),
params,
MachineErrorParams.builder().machine(MachineType.COMPLETE_GENOMICS).create(),
null);
fail();
} catch (final NoTalkbackSlimException e) {
assertTrue(e.getMessage(), e.getMessage().startsWith("Invalid CG alignment."));
}
}
public void test() {
final SAMRecord rec = new SAMRecord(new SAMFileHeader());
rec.setReadString("TATTAGGATTGAGACTGGTAAAATGGNCCACCAAG");
rec.setBaseQualityString("/725361840-525251.68,0,.52!222254/2");
rec.setReadPairedFlag(true);
final VariantParams params = VariantParams.builder().create();
final AbstractMachineErrorParams me =
MachineErrorParams.builder().machine(MachineType.COMPLETE_GENOMICS).create();
final AlignmentEnvironment se =
new AlignmentEnvironmentCG(new VariantAlignmentRecord(rec), params, me, null);
assertFalse(!se.isInverted());
final String exp =
""
+ "AlignmentEnvironment read=GAACCACCNGGTAAAATGGTCAGAGTTAGGATTAT "
+ "quality=["
+ "0.0200, 0.0398, 0.0126, 0.0100, 0.0200, 0.0200, 0.0200, 0.0200, 1.0000, 0.0200, "
+ "0.0100, 0.0501, 0.0794, 0.0316, 0.0794, 0.0050, 0.0079, 0.0501, 0.0251, 0.0100, "
+ "0.0200, 0.0100, 0.0200, 0.0100, 0.0631, 0.0316, 0.0126, 0.0050, 0.0251, 0.0079, "
+ "0.0158, 0.0100, 0.0200, 0.0063, 0.0398"
+ "] start=-1";
assertEquals(exp, se.toString());
}
public void testDefaultQuality() {
final SAMRecord rec = new SAMRecord(new SAMFileHeader());
rec.setReadString("TATTAGGATTGAGACTGGTAAAATGGNCCACCAAG");
rec.setReadPairedFlag(true);
final VariantParams params = VariantParams.builder().defaultQuality(10).create();
final AlignmentEnvironment se =
new AlignmentEnvironmentCG(
new VariantAlignmentRecord(rec),
params,
MachineErrorParams.builder().machine(MachineType.COMPLETE_GENOMICS).create(),
null);
assertFalse(!se.isInverted());
final String exp =
""
+ "AlignmentEnvironment read=GAACCACCNGGTAAAATGGTCAGAGTTAGGATTAT "
+ "quality=["
+ "0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, "
+ "0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, "
+ "0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, 0.1000, "
+ "0.1000, 0.1000, 0.1000, 0.1000, 0.1000"
+ "] start=-1";
assertEquals(exp, se.toString());
}