private void collectQualityData(final SAMRecord record, final ReferenceSequence reference) {
// If the read isnt an aligned PF read then look at the read for no-calls
if (record.getReadUnmappedFlag()
|| record.getReadFailsVendorQualityCheckFlag()
|| !doRefMetrics) {
final byte[] readBases = record.getReadBases();
for (int i = 0; i < readBases.length; i++) {
if (SequenceUtil.isNoCall(readBases[i])) {
badCycleHistogram.increment(
CoordMath.getCycle(record.getReadNegativeStrandFlag(), readBases.length, i));
}
}
} else if (!record.getReadFailsVendorQualityCheckFlag()) {
final boolean highQualityMapping = isHighQualityMapping(record);
if (highQualityMapping) metrics.PF_HQ_ALIGNED_READS++;
final byte[] readBases = record.getReadBases();
final byte[] refBases = reference.getBases();
final byte[] qualities = record.getBaseQualities();
final int refLength = refBases.length;
long mismatchCount = 0;
long hqMismatchCount = 0;
for (final AlignmentBlock alignmentBlock : record.getAlignmentBlocks()) {
final int readIndex = alignmentBlock.getReadStart() - 1;
final int refIndex = alignmentBlock.getReferenceStart() - 1;
final int length = alignmentBlock.getLength();
for (int i = 0; i < length && refIndex + i < refLength; ++i) {
final int readBaseIndex = readIndex + i;
boolean mismatch =
!SequenceUtil.basesEqual(readBases[readBaseIndex], refBases[refIndex + i]);
boolean bisulfiteBase = false;
if (mismatch && isBisulfiteSequenced) {
if ((record.getReadNegativeStrandFlag()
&& (refBases[refIndex + i] == 'G' || refBases[refIndex + i] == 'g')
&& (readBases[readBaseIndex] == 'A' || readBases[readBaseIndex] == 'a'))
|| ((!record.getReadNegativeStrandFlag())
&& (refBases[refIndex + i] == 'C' || refBases[refIndex + i] == 'c')
&& (readBases[readBaseIndex] == 'T')
|| readBases[readBaseIndex] == 't')) {
bisulfiteBase = true;
mismatch = false;
}
}
if (mismatch) mismatchCount++;
metrics.PF_ALIGNED_BASES++;
if (!bisulfiteBase) nonBisulfiteAlignedBases++;
if (highQualityMapping) {
metrics.PF_HQ_ALIGNED_BASES++;
if (!bisulfiteBase) hqNonBisulfiteAlignedBases++;
if (qualities[readBaseIndex] >= BASE_QUALITY_THRESHOLD)
metrics.PF_HQ_ALIGNED_Q20_BASES++;
if (mismatch) hqMismatchCount++;
}
if (mismatch || SequenceUtil.isNoCall(readBases[readBaseIndex])) {
badCycleHistogram.increment(
CoordMath.getCycle(record.getReadNegativeStrandFlag(), readBases.length, i));
}
}
}
mismatchHistogram.increment(mismatchCount);
hqMismatchHistogram.increment(hqMismatchCount);
// Add any insertions and/or deletions to the global count
for (final CigarElement elem : record.getCigar().getCigarElements()) {
final CigarOperator op = elem.getOperator();
if (op == CigarOperator.INSERTION || op == CigarOperator.DELETION) ++this.indels;
}
}
}
public void find_coverage(SAMResource sres) {
int start_base = sres.region.range.start;
int end_base = sres.region.range.end;
int coverage_len = (end_base - start_base) + 1;
int i, end, ref_i, read_i, len;
int[] coverage = new int[coverage_len];
Arrays.fill(coverage, 0);
WorkingFile wf = null;
if (outfile != null) {
try {
wf = new WorkingFile(outfile);
ps = wf.getPrintStream();
} catch (Exception e) {
System.err.println("I/O error: " + e); // debug
e.printStackTrace();
System.exit(1);
}
}
try {
//
// gather coverage info:
//
CloseableIterator<SAMRecord> iterator = sres.get_iterator();
int read_count = 0;
int ref_min = -1;
int ref_max = -1;
while (iterator.hasNext()) {
SAMRecord sr = iterator.next();
read_count++;
// System.err.println(sr.getReadName() + ": " + sr.getAlignmentStart() + "-" +
// sr.getAlignmentEnd()); // debug
if (sr.getReadUnmappedFlag()) continue;
if (sr.getDuplicateReadFlag()) {
if (verbose_mode)
System.err.println(
sr.getReadName()
+ "."
+ (sr.getReadNegativeStrandFlag() ? "R" : "F")
+ " ignoring, duplicate");
continue;
}
byte[] read = sr.getReadBases();
byte[] quals = sr.getBaseQualities();
for (AlignmentBlock ab : sr.getAlignmentBlocks()) {
len = ab.getLength();
read_i = ab.getReadStart() - 1;
ref_i = ab.getReferenceStart() - start_base;
if (ref_min == -1 || ref_i < ref_min) ref_min = ref_i;
for (i = read_i, end = read_i + len; i < end; i++, ref_i++) {
if (ref_i >= 0 && ref_i < coverage_len) {
if (quals[i] >= MIN_QUALITY) {
if (verbose_mode)
System.err.println(
sr.getReadName()
+ "."
+ (sr.getReadNegativeStrandFlag() ? "R" : "F")
+ " hit at "
+ (ref_i + start_base)
+ " as="
+ sr.getAlignmentStart()
+ " ae="
+ sr.getAlignmentEnd());
coverage[ref_i]++;
} else if (verbose_mode) {
System.err.println(
sr.getReadName()
+ "."
+ (sr.getReadNegativeStrandFlag() ? "R" : "F")
+ " qual_reject at "
+ (ref_i + start_base)
+ " as="
+ sr.getAlignmentStart()
+ " ae="
+ sr.getAlignmentEnd());
}
}
}
if (ref_max == -1 || ref_i > ref_max) ref_max = ref_i;
}
}
sres.close();
System.err.println(
"records:"
+ read_count
+ " ref_min:"
+ (ref_min + start_base)
+ " ref_max:"
+ (ref_max + start_base)); // debug
//
// report coverage info:
//
for (i = 0; i < coverage.length; i++) {
if (name != null) ps.print(name + ",");
ps.println((i + start_base) + "," + coverage[i]); // debug
}
if (wf != null) wf.finish();
} catch (Exception e) {
System.err.println("ERROR: " + e); // debug
e.printStackTrace();
}
}