@Override
protected void runImpl() throws ExecutionFailedException {
info("Loading...");
ArrayList<Dna> reads;
// ToDo: rewrite it to use normal reader
try {
reads = ReadsPlainReader.loadReads(readsFile.get().getPath());
} catch (IOException e) {
throw new ExecutionFailedException(e);
}
info("Creating string...");
GluedDnasString string = GluedDnasString.createGluedDnasString(reads);
info("Full string length = " + groupDigits(string.length));
info("Dumping...");
string.dump(fullStringFile.get());
}
@Override
protected void runImpl() throws ExecutionFailedException {
outputDir.get().mkdir();
Iterator<File> originalReadsIterator = Arrays.asList(originalReads.get()).iterator();
Iterator<File> correctedReadsIterator = Arrays.asList(correctedReads.get()).iterator();
for (Iterator<UniPair<File>> it =
new UniZippingIterator<File>(originalReadsIterator, correctedReadsIterator);
it.hasNext(); ) {
UniPair<File> cur = it.next();
BinqReader initial = null;
try {
initial = new BinqReader(cur.first);
} catch (IOException e) {
throw new ExecutionFailedException("Can't create library from from file " + cur.first, e);
}
BinqReader fixed = null;
try {
fixed = new BinqReader(cur.second);
} catch (IOException e) {
throw new ExecutionFailedException("Can't create library from from file " + cur.second, e);
}
String fn = (new File(initial.name())).getName();
// System.err.println("fn = " + fn);
try {
IOUtils.dnaQs2BinqFile(
new MergeIterator(fixed.iterator(), initial.iterator()),
outputDir.get() + File.separator + initial.name() + ".binq",
false);
} catch (IOException e) {
throw new ExecutionFailedException(e);
}
}
}