/**
* The main member function for dispensing patterns.
*
* Returns true iff a pair was parsed succesfully.
*/
bool PatternSource::nextReadPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired,
bool fixName)
{
// nextPatternImpl does the reading from the ultimate source;
// it is implemented in concrete subclasses
success = done = paired = false;
nextReadPairImpl(ra, rb, rdid, endid, success, done, paired);
if(success) {
// Construct reversed versions of fw and rc seqs/quals
ra.finalize();
if(!rb.empty()) {
rb.finalize();
}
// Fill in the random-seed field using a combination of
// information from the user-specified seed and the read
// sequence, qualities, and name
ra.seed = genRandSeed(ra.patFw, ra.qual, ra.name, seed_);
if(!rb.empty()) {
rb.seed = genRandSeed(rb.patFw, rb.qual, rb.name, seed_);
}
}
return success;
}
/**
* The main member function for dispensing patterns.
*/
bool PatternSource::nextRead(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done)
{
// nextPatternImpl does the reading from the ultimate source;
// it is implemented in concrete subclasses
nextReadImpl(r, rdid, endid, success, done);
if(success) {
// Construct the reversed versions of the fw and rc seqs
// and quals
r.finalize();
// Fill in the random-seed field using a combination of
// information from the user-specified seed and the read
// sequence, qualities, and name
r.seed = genRandSeed(r.patFw, r.qual, r.name, seed_);
}
return success;
}
