/**
* 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
public void testPerReadAlleleLikelihoodMap() {
final PerReadAlleleLikelihoodMap map = new PerReadAlleleLikelihoodMap();
final Allele alleleA = Allele.create("A");
final double lik = -1.0; // ignored
final int[] MQs = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, QualityUtils.MAPPING_QUALITY_UNAVAILABLE};
final List<Integer> MQsList = Arrays.asList(ArrayUtils.toObject(MQs));
// MQ 255 are excluded from the calculations, we test it here.
final List<Integer> MQsListOK = new ArrayList<>(MQsList);
// NOTE: if we just call remove(i), Java thinks i is an index.
// A workaround for this overloading bogosity to to call removeAll and pass a collection
// (casting i to (Object) would work too but it's more error prone)
MQsListOK.removeAll(Collections.singleton(QualityUtils.MAPPING_QUALITY_UNAVAILABLE));
final int n1A = MQs.length;
for (int i = 0; i < n1A; i++) {
final GATKRead read = ArtificialReadUtils.createArtificialRead(TextCigarCodec.decode("10M"));
read.setMappingQuality(MQs[i]);
map.add(read, alleleA, lik);
}
final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap =
Collections.singletonMap("sample1", map);
final VariantContext vc = makeVC();
final ReferenceContext referenceContext = null;
final Map<String, Object> annotate =
new RMSMappingQuality().annotate(referenceContext, vc, perReadAlleleLikelihoodMap);
Assert.assertEquals(annotate.size(), 1, "size");
Assert.assertEquals(
annotate.keySet(), Collections.singleton(VCFConstants.RMS_MAPPING_QUALITY_KEY), "annots");
final double rms = MathUtils.rms(MQsListOK); // only those are MQ0
Assert.assertEquals(
annotate.get(VCFConstants.RMS_MAPPING_QUALITY_KEY), String.format("%.2f", rms));
}
