/**
* The main member function for dispensing pairs of reads or
* singleton reads. Returns true iff ra and rb contain a new
* pair; returns false if ra contains a new unpaired read.
*/
bool PairedSoloPatternSource::nextReadPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired,
bool fixName)
{
// printf("paired solo pattern source\n");
uint32_t cur = cur_;
success = false;
while(cur < src_->size()) {
// Patterns from srca_[cur_] are unpaired
do {
(*src_)[cur]->nextReadPair(
ra, rb, rdid, endid, success, done, paired, fixName);
} while(!success && !done);
if(!success) {
assert(done);
// If patFw is empty, that's our signal that the
// input dried up
lock();
if(cur + 1 > cur_) cur_++;
cur = cur_;
unlock();
continue; // on to next pair of PatternSources
}
assert(success);
ra.seed = genRandSeed(ra.patFw, ra.qual, ra.name, seed_);
if(!rb.empty()) {
rb.seed = genRandSeed(rb.patFw, rb.qual, rb.name, seed_);
if(fixName) {
ra.fixMateName(1);
rb.fixMateName(2);
}
}
ra.rdid = rdid;
ra.endid = endid;
if(!rb.empty()) {
rb.rdid = rdid;
rb.endid = endid+1;
}
ra.mate = 1;
rb.mate = 2;
return true; // paired
}
assert_leq(cur, src_->size());
done = (cur == src_->size());
return false;
}
/**
* Once name/sequence/qualities have been parsed for a
* paired-end read, set all the other key fields of the Read
* structs.
*/
void PatternSourcePerThread::finalizePair(Read& ra, Read& rb) {
ra.mate = 1;
ra.constructRevComps();
ra.constructReverses();
ra.fixMateName(1);
ra.seed = genRandSeed(ra.patFw, ra.qual, ra.name, seed_);
rb.mate = 2;
rb.constructRevComps();
rb.constructReverses();
rb.fixMateName(2);
rb.seed = genRandSeed(rb.patFw, rb.qual, rb.name, seed_);
}
/**
* The main member function for dispensing pairs of reads or
* singleton reads. Returns true iff ra and rb contain a new
* pair; returns false if ra contains a new unpaired read.
*/
bool PairedDualPatternSource::nextReadPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired,
bool fixName)
{
// 'cur' indexes the current pair of PatternSources
uint32_t cur;
{
lock();
cur = cur_;
unlock();
}
success = false;
done = true;
while(cur < srca_->size()) {
if((*srcb_)[cur] == NULL) {
paired = false;
// Patterns from srca_ are unpaired
do {
(*srca_)[cur]->nextRead(ra, rdid, endid, success, done);
} while(!success && !done);
if(!success) {
assert(done);
lock();
if(cur + 1 > cur_) cur_++;
cur = cur_; // Move on to next PatternSource
unlock();
continue; // on to next pair of PatternSources
}
ra.rdid = rdid;
ra.endid = endid;
ra.mate = 0;
return success;
} else {
paired = true;
// Patterns from srca_[cur_] and srcb_[cur_] are paired
TReadId rdid_a = 0, endid_a = 0;
TReadId rdid_b = 0, endid_b = 0;
bool success_a = false, done_a = false;
bool success_b = false, done_b = false;
// Lock to ensure that this thread gets parallel reads
// in the two mate files
lock();
do {
(*srca_)[cur]->nextRead(ra, rdid_a, endid_a, success_a, done_a);
} while(!success_a && !done_a);
do {
(*srcb_)[cur]->nextRead(rb, rdid_b, endid_b, success_b, done_b);
} while(!success_b && !done_b);
if(!success_a && success_b) {
cerr << "Error, fewer reads in file specified with -1 than in file specified with -2" << endl;
throw 1;
} else if(!success_a) {
assert(done_a && done_b);
if(cur + 1 > cur_) cur_++;
cur = cur_; // Move on to next PatternSource
unlock();
continue; // on to next pair of PatternSources
} else if(!success_b) {
cerr << "Error, fewer reads in file specified with -2 than in file specified with -1" << endl;
throw 1;
}
assert_eq(rdid_a, rdid_b);
//assert_eq(endid_a+1, endid_b);
assert_eq(success_a, success_b);
unlock();
if(fixName) {
ra.fixMateName(1);
rb.fixMateName(2);
}
rdid = rdid_a;
endid = endid_a;
success = success_a;
done = done_a;
ra.rdid = rdid;
ra.endid = endid;
if(!rb.empty()) {
rb.rdid = rdid;
rb.endid = endid+1;
}
ra.mate = 1;
rb.mate = 2;
return success;
}
}
return success;
}
/**
* The main member function for dispensing pairs of reads or
* singleton reads. Returns true iff ra and rb contain a new
* pair; returns false if ra contains a new unpaired read.
*/
bool PairedDualPatternSource::nextReadPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired,
bool fixName)
{
//std::cout << "PairedDualPatternSource::nextReadPair\n";
// 'cur' indexes the current pair of PatternSources
// struct timeval t1, t2;
// double elapsedTime = 0;
uint32_t cur;
{
//lock();
cur = cur_;
//unlock();
}
success = false;
done = true;
while(cur < srca_->size()) {
if((*srcb_)[cur] == NULL) {
paired = false;
// Patterns from srca_ are unpaired
do {
// gettimeofday(&t1, NULL);
(*srca_)[cur]->nextRead(ra, rdid, endid, success, done);
// gettimeofday(&t2, NULL);
// elapsedTime = (t2.tv_sec - t1.tv_sec) * 1000.0; // sec to ms
// elapsedTime += (t2.tv_usec - t1.tv_usec) / 1000.0; // us to ms
// printf("time elapsed in PairedDualPatternSource::nextReadPair %f\n", elapsedTime);
} while(!success && !done);
if(!success) {
assert(done);
//lock();
if(cur + 1 > cur_) cur_++;
cur = cur_; // Move on to next PatternSource
//unlock();
continue; // on to next pair of PatternSources
}
ra.rdid = rdid;
ra.endid = endid;
ra.mate = 0;
return success;
} else {
paired = true;
// Patterns from srca_[cur_] and srcb_[cur_] are paired
TReadId rdid_a = 0, endid_a = 0;
TReadId rdid_b = 0, endid_b = 0;
bool success_a = false, done_a = false;
bool success_b = false, done_b = false;
// Lock to ensure that this thread gets parallel reads
// in the two mate files
//lock();
do {
(*srca_)[cur]->nextRead(ra, rdid_a, endid_a, success_a, done_a);
} while(!success_a && !done_a);
do {
(*srcb_)[cur]->nextRead(rb, rdid_b, endid_b, success_b, done_b);
} while(!success_b && !done_b);
if(!success_a && success_b) {
cerr << "Error, fewer reads in file specified with -1 than in file specified with -2" << endl;
throw 1;
} else if(!success_a) {
assert(done_a && done_b);
if(cur + 1 > cur_) cur_++;
cur = cur_; // Move on to next PatternSource
//unlock();
continue; // on to next pair of PatternSources
} else if(!success_b) {
cerr << "Error, fewer reads in file specified with -2 than in file specified with -1" << endl;
throw 1;
}
assert_eq(rdid_a, rdid_b);
//assert_eq(endid_a+1, endid_b);
assert_eq(success_a, success_b);
//unlock();
if(fixName) {
ra.fixMateName(1);
rb.fixMateName(2);
}
rdid = rdid_a;
endid = endid_a;
success = success_a;
done = done_a;
ra.rdid = rdid;
ra.endid = endid;
if(!rb.empty()) {
rb.rdid = rdid;
rb.endid = endid+1;
}
ra.mate = 1;
rb.mate = 2;
return success;
}
}
return success;
}
