/**
* 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();
}
public void writeSeq(Sequence s) {
writeSeq(s.getSeqName(), s.getDesc(), s.getSeqString());
}
private synchronized void writeSeq(Sequence seq, PrintStream outStream) {
outStream.println(">" + seq.getSeqName() + "\n" + seq.getSeqString());
}