@Test(enabled = true) public void testCheckSeqStored () { final GATKSAMRecord goodRead = ArtificialSAMUtils.createArtificialRead(new byte[]{(byte)'A'}, new byte[]{(byte)'A'}, "1M"); final GATKSAMRecord badRead = ArtificialSAMUtils.createArtificialRead(new byte[]{}, new byte[]{}, "1M"); badRead.setReadString("*"); Assert.assertTrue(MalformedReadFilter.checkSeqStored(goodRead, true)); Assert.assertFalse(MalformedReadFilter.checkSeqStored(badRead, true)); try { MalformedReadFilter.checkSeqStored(badRead, false); Assert.assertTrue(false, "We should have exceptioned out in the previous line"); } catch (UserException e) { } }
protected GATKSAMRecord buildSAMRecord(final String readName, final String contig, final int alignmentStart) { GATKSAMRecord record = new GATKSAMRecord(header); record.setReadName(readName); record.setReferenceIndex(dictionary.getSequenceIndex(contig)); record.setAlignmentStart(alignmentStart); record.setCigarString("1M"); record.setReadString("A"); record.setBaseQualityString("A"); record.setReadGroup(readGroup); return record; }
protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) { SAMFileHeader header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test"); header.setSequenceDictionary(dictionary); header.setSortOrder(SAMFileHeader.SortOrder.coordinate); GATKSAMRecord record = new GATKSAMRecord(header); record.setReadName(readName); record.setReferenceIndex(dictionary.getSequenceIndex(contig)); record.setAlignmentStart(alignmentStart); Cigar cigar = new Cigar(); int len = alignmentEnd - alignmentStart + 1; cigar.add(new CigarElement(len, CigarOperator.M)); record.setCigar(cigar); record.setReadString(new String(new char[len]).replace("\0", "A")); record.setBaseQualities(new byte[len]); record.setReadGroup(new GATKSAMReadGroupRecord(header.getReadGroup("test"))); return record; }
correctedRead.setIsStrandless(inputRead.isStrandless()); correctedRead.setReadBases(inputRead.getReadBases()); correctedRead.setReadString(inputRead.getReadString()); correctedRead.setReadGroup(inputRead.getReadGroup()); return correctedRead;