/**
* Decode a single line in a SAM text file.
*
* @param line line to decode.
* @return A SAMReadFeature modeling that line.
*/
@Override
public SAMReadFeature decode(String line) {
// we may be asked to process a header line; ignore it
if (line.startsWith("@")) return null;
String[] tokens = new String[expectedTokenCount];
// split the line
int count = ParsingUtils.splitWhitespace(line, tokens);
// check to see if we've parsed the string into the right number of tokens (expectedTokenCount)
if (count != expectedTokenCount)
throw new CodecLineParsingException(
"the SAM read line didn't have the expected number of tokens "
+ "(expected = "
+ expectedTokenCount
+ ", saw = "
+ count
+ " on "
+ "line = "
+ line
+ ")");
final String readName = tokens[0];
final int flags = Integer.parseInt(tokens[1]);
final String contigName = tokens[2];
final int alignmentStart = Integer.parseInt(tokens[3]);
final int mapQ = Integer.parseInt(tokens[4]);
final String cigarString = tokens[5];
final String mateContigName = tokens[6];
final int mateAlignmentStart = Integer.parseInt(tokens[7]);
final int inferredInsertSize = Integer.parseInt(tokens[8]);
final byte[] bases = StringUtil.stringToBytes(tokens[9]);
final byte[] qualities = StringUtil.stringToBytes(tokens[10]);
// Infer the alignment end.
Cigar cigar = TextCigarCodec.decode(cigarString);
int alignmentEnd = alignmentStart + cigar.getReferenceLength() - 1;
// Remove printable character conversion from the qualities.
for (byte quality : qualities) quality -= 33;
return new SAMReadFeature(
readName,
flags,
contigName,
alignmentStart,
alignmentEnd,
mapQ,
cigarString,
mateContigName,
mateAlignmentStart,
inferredInsertSize,
bases,
qualities);
}
@Test(expectedExceptions = {SAMException.class})
public void testUnmergeableSequenceDictionary() {
final String sd1 = sq1 + sq2 + sq5;
final String sd2 = sq2 + sq3 + sq4 + sq1;
SAMFileReader reader1 =
new SAMFileReader(new ByteArrayInputStream(StringUtil.stringToBytes(sd1)));
SAMFileReader reader2 =
new SAMFileReader(new ByteArrayInputStream(StringUtil.stringToBytes(sd2)));
final List<SAMFileHeader> inputHeaders =
Arrays.asList(reader1.getFileHeader(), reader2.getFileHeader());
new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate, inputHeaders, true);
}
@Test
public void testSequenceDictionaryMerge() {
final String sd1 = sq1 + sq2 + sq5;
final String sd2 = sq2 + sq3 + sq4;
SAMFileReader reader1 =
new SAMFileReader(new ByteArrayInputStream(StringUtil.stringToBytes(sd1)));
SAMFileReader reader2 =
new SAMFileReader(new ByteArrayInputStream(StringUtil.stringToBytes(sd2)));
final List<SAMFileHeader> inputHeaders =
Arrays.asList(reader1.getFileHeader(), reader2.getFileHeader());
SamFileHeaderMerger merger =
new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate, inputHeaders, true);
final SAMFileHeader mergedHeader = merger.getMergedHeader();
for (final SAMFileHeader inputHeader : inputHeaders) {
int prevTargetIndex = -1;
for (final SAMSequenceRecord sequenceRecord :
inputHeader.getSequenceDictionary().getSequences()) {
final int targetIndex = mergedHeader.getSequenceIndex(sequenceRecord.getSequenceName());
Assert.assertNotSame(targetIndex, -1);
Assert.assertTrue(prevTargetIndex < targetIndex);
prevTargetIndex = targetIndex;
}
}
}
