/**
* This need to be thread safe
*
* @param seq
* @param outStream
* @throws IOException
*/
private void processReads(Sequence seq, PrintStream outStream) throws IOException {
NuclKmerGenerator kmerGenerator;
Kmer kmer;
boolean found = false;
kmerGenerator = new NuclKmerGenerator(seq.getSeqString(), kmerSize);
while (kmerGenerator.hasNext()) {
kmer = kmerGenerator.next();
for (int i = 0; i < kmerMaps.length; i++) { // for forward and reverse direction
KmerAbund kmerAbund = kmerMaps[i].get(kmer);
if (kmerAbund != null) {
// increment the count
kmerAbund.count.addAndGet(1);
found = true;
}
}
}
if (found) {
totalReads.incrementAndGet();
}
if (outStream != null && found) {
writeSeq(seq, outStream);
}
}
/**
* find the kmers in the contigs
*
* @param reader
* @throws IOException
*/
private void processContigFile(SequenceReader reader) throws IOException {
Sequence seq;
NuclKmerGenerator kmerGenerator;
Kmer kmer;
int contigIdx = 0;
while ((seq = reader.readNextSequence()) != null) {
if (seq.getSeqString().length() < kmerSize) {
continue;
}
// use int to represent seqname in case contig names are too long
contigMap.put(
contigIdx, new Contig(seq.getSeqName(), seq.getSeqString().length() - kmerSize + 1));
// forward direction
kmerGenerator = new NuclKmerGenerator(seq.getSeqString(), kmerSize);
while (kmerGenerator.hasNext()) {
kmer = kmerGenerator.next();
KmerAbund kmerAbund = kmerMaps[0].get(kmer);
if (kmerAbund == null) {
kmerAbund = new KmerAbund();
kmerMaps[0].put(kmer, kmerAbund);
}
kmerAbund.contigList.add(new ContigCoverage(contigIdx, kmerGenerator.getPosition() - 1));
}
// reverse direction
kmerGenerator =
new NuclKmerGenerator(IUBUtilities.reverseComplement(seq.getSeqString()), kmerSize);
while (kmerGenerator.hasNext()) {
kmer = kmerGenerator.next();
KmerAbund kmerAbund = kmerMaps[1].get(kmer);
if (kmerAbund == null) {
kmerAbund = new KmerAbund();
kmerMaps[1].put(kmer, kmerAbund);
}
kmerAbund.contigList.add(
new ContigCoverage(
contigIdx,
seq.getSeqString().length() - kmerGenerator.getPosition() - kmerSize + 1));
}
contigIdx++;
}
reader.close();
}