NROption::NROption(const string& version) :
version(version), all("\nnr " + version + "\n\nUsage"), popt() {
opt other("Other");
opt input("Input");
opt output("Output");
opt qualities("Qualities");
other.add_options()
("help,h", "show the usage")
("verbose", "show progress when possible")
("version", "output the version number");
input.add_options()
("data,d", po::value<string>(), "data file")
("control,c", po::value<string>(), "control file")
("format", po::value<string>(),
"the format of the data file, can be one of : "
"bowtie, sam, bam and bed");
qualities.add_options()
("ext_length,l", po::value<uint32_t>()->default_value(200),
"read extension length");
popt.add("data", 1).add("control", 1);
all.add(input).add(qualities).add(other);
}
std::vector<float> DestinNetworkAlt::getLayersQualities()
{
std::vector<float> qualities(destin->nLayers);
for (int i = 0; i < destin->nLayers; i++)
{
qualities[i] = getQuality(i);
}
return qualities;
}
break;
}
}
for (j = q2len-1; j > 0 ; j--) {
if (((int)qual2[j] - 33) >= minQ ){
val.right_trim = j+1; // add 1 as i is the first good base
break;
}
}
return (val);
}
PyDoc_STRVAR(trimseq_doc,
"trim(qual1, qual2, minQ) -> int, int\n\
Determines the first postion from both qualities (from the end) at which the cooresponding quality value is >= minQ and returns those positions\n");
static PyObject *
trimseq(PyObject *self, PyObject *args)
{
Tuple r;
char *a, *b;
int alen, blen, m;
if (!PyArg_ParseTuple(args, "s#s#i", &a, &alen, &b, &blen, &m))
return NULL;
r = trim_sequence(a, alen, b, blen, m);
if (r.left_trim== -1) {
PyErr_SetString(PyExc_MemoryError, "Out of memory");
return NULL;
}
