@Override
public void execute() {
TableReader tr = new TableReader(KMER_REFERENCE_PANEL);
Set<CortexKmer> kmers = new HashSet<CortexKmer>();
int kmerSize = 0;
for (Map<String, String> te : tr) {
CortexKmer kmer = new CortexKmer(te.get("kmer"));
kmers.add(kmer);
if (kmerSize == 0) {
kmerSize = kmer.length();
}
}
ReferenceSequence rseq;
while ((rseq = SUPERNODES.nextSequence()) != null) {
String seq = new String(rseq.getBases());
for (int i = 0; i <= seq.length() - kmerSize; i++) {
CortexKmer kmer = new CortexKmer(seq.substring(i, i + kmerSize));
if (kmers.contains(kmer)) {
out.println(">" + rseq.getName() + "\n" + seq);
break;
}
}
}
}
@Override
public void execute() {
ReferenceSequence rseq;
while ((rseq = REF.nextSequence()) != null) {
String seq = new String(rseq.getBases());
for (int i = 0; i + LENGTH < rseq.length(); i += LENGTH) {
String slice = seq.substring(i, i + LENGTH);
out.println(">" + rseq.getName() + "." + i);
out.println(slice);
}
}
}
private void loadContigs() {
if (contigs == null || contigs.size() == 0) {
contigs = new HashMap<String, String>();
TableReader tr = new TableReader(METRICS);
metrics = new HashMap<String, Map<String, String>>();
for (Map<String, String> te : tr) {
String contigName = te.get("contigName");
String seq = te.get("seq");
contigs.put(contigName, seq);
metrics.put(contigName, te);
}
}
FastaSequenceFile fasta = new FastaSequenceFile(CONTIGS, false);
ReferenceSequence rseq;
while ((rseq = fasta.nextSequence()) != null) {
String[] name = rseq.getName().split("\\s+");
contigs.put(name[0], new String(rseq.getBases()));
}
}
public GeneralizedSequenceReader(File file) {
if (file.getName().endsWith(".bam")) {
sfr = new SAMFileReader(file);
sfr.setValidationStringency(ValidationStringency.SILENT);
} else if (file.getName().endsWith(".fastq")
|| file.getName().endsWith(".fq")
|| file.getName().endsWith(".fastq.gz")
|| file.getName().endsWith(".fq.gz")) {
fqr = new FastqReader(file, true);
} else if (file.getName().endsWith(".fasta") || file.getName().endsWith(".fa")) {
fsr = new FastaSequenceFile(file, false);
fss = new LinkedHashSet<String>();
ReferenceSequence rseq;
while ((rseq = fsr.nextSequence()) != null) {
fss.add(new String(rseq.getBases()));
}
} else {
throw new IndianaException(
"Cannot parse '" + file.getAbsolutePath() + "' with generalized reader");
}
}