/**
* Test the parsing of sequence variations from Last MAF file.
*
* @throws IOException
*/
@Test
public void testLastToCompactVariations() throws IOException {
// test LastToCompact convert+filtering
// read fake data and convert+filter
final LastToCompactMode processor = new LastToCompactMode();
final int LAST_TO_COMPACT_M_PARAM = 2;
processor.setAmbiguityThreshold(LAST_TO_COMPACT_M_PARAM);
processor.setInputFile("test-results/alignments/last-to-compact/last-103-variations.maf");
processor.setOutputFile("test-results/alignments/last-to-compact/last-103-variations");
processor.setTargetReferenceIdsFilename(
"test-results/alignments/last-to-compact/last-reference.compact-reads");
processor.setOnlyMafFile(true);
processor.setNumberOfReads(2857822);
processor.setLargestQueryIndex(2857822);
processor.setSmallestQueryIndex(0);
processor.setPropagateQueryIds(false);
processor.setPropagateTargetIds(true);
processor.setQualityFilterParameters(
"threshold=1"); // allow everything to pass through, important to detect all variations in
// this test.
processor.execute();
// read compact alignment results
final AlignmentReaderImpl reader = new AlignmentReaderImpl(processor.getOutputFile());
reader.readHeader();
assertEquals(2857822, reader.getNumberOfQueries());
assertEquals(1, reader.getNumberOfTargets());
int entryIndex = 0;
while (reader.hasNext()) {
final Alignments.AlignmentEntry alignmentEntry = reader.next();
System.out.println(entryIndex + " entry : " + alignmentEntry);
switch (entryIndex) {
case 0:
assertEquals(2, alignmentEntry.getSequenceVariationsCount());
final Alignments.SequenceVariation var1 = alignmentEntry.getSequenceVariations(0);
assertEquals("C", var1.getTo());
assertEquals("G", var1.getFrom());
assertEquals(1, var1.getPosition());
final Alignments.SequenceVariation var2 = alignmentEntry.getSequenceVariations(1);
assertEquals("C", var2.getTo());
assertEquals("A", var2.getFrom());
assertEquals(11, var2.getPosition());
break;
case 1:
assertEquals(1, alignmentEntry.getSequenceVariationsCount());
final Alignments.SequenceVariation var1_0 = alignmentEntry.getSequenceVariations(0);
assertEquals("---", var1_0.getTo());
assertEquals("TTT", var1_0.getFrom());
assertEquals(3, var1_0.getPosition());
break;
case 2:
assertEquals(2, alignmentEntry.getSequenceVariationsCount());
final Alignments.SequenceVariation var2_1 = alignmentEntry.getSequenceVariations(0);
assertEquals("A", var2_1.getTo());
assertEquals("G", var2_1.getFrom());
assertEquals(2, var2_1.getPosition());
final Alignments.SequenceVariation var2_2 = alignmentEntry.getSequenceVariations(1);
assertEquals("A", var2_2.getTo());
assertEquals("-", var2_2.getFrom());
assertEquals(29, var2_2.getPosition());
break;
default:
break;
}
entryIndex++;
}
assertEquals(4, entryIndex);
}
