| 173 |
|
|
| 174 |
|
bool next_fastx_read(FLineReader& fr, Read& read, ReadFormat reads_format, |
| 175 |
|
FLineReader* frq) { |
| 176 |
+ |
/* |
| 177 |
|
if (fr.pushed_read) |
| 178 |
|
{ |
| 179 |
|
read = fr.last_read; |
| 180 |
|
fr.pushed_read = false; |
| 181 |
|
return true; |
| 182 |
|
} |
| 183 |
< |
|
| 183 |
> |
*/ |
| 184 |
|
read.clear(); |
| 185 |
|
char* buf=NULL; |
| 186 |
|
while ((buf=fr.nextLine())!=NULL) { |
| 263 |
|
} |
| 264 |
|
} |
| 265 |
|
|
| 266 |
< |
fr.last_read = read; |
| 266 |
> |
//fr.last_read = read; |
| 267 |
|
return !(read.seq.empty()); |
| 268 |
|
} |
| 269 |
|
|
| 595 |
|
} |
| 596 |
|
|
| 597 |
|
|
| 598 |
+ |
void bam2Read(bam1_t *b, Read& rd, bool alt_name=false) { |
| 599 |
+ |
GBamRecord bamrec(b); |
| 600 |
+ |
rd.clear(); |
| 601 |
+ |
rd.seq=bamrec.seqData(&rd.qual); |
| 602 |
+ |
rd.name=bam1_qname(b); |
| 603 |
+ |
if (alt_name) |
| 604 |
+ |
rd.alt_name=bamrec.tag_str("XA"); |
| 605 |
+ |
} |
| 606 |
+ |
|
| 607 |
+ |
|
| 608 |
|
bool ReadStream::next_read(Read& r, ReadFormat read_format) { |
| 609 |
< |
FLineReader fr(fstream.file); |
| 599 |
< |
while (read_pq.size()<500000 && !r_eof) { |
| 609 |
> |
while (read_pq.size()<ReadBufSize && !r_eof) { |
| 610 |
|
//keep the queue topped off |
| 611 |
|
Read rf; |
| 612 |
< |
if (!next_fastx_read(fr, rf, read_format)) { |
| 612 |
> |
if (fstream.is_bam) { |
| 613 |
> |
if (samread(fstream.bam_file, b) < 0) { |
| 614 |
|
r_eof=true; |
| 615 |
|
break; |
| 616 |
|
} |
| 617 |
< |
//Read read=Read(rf); |
| 617 |
> |
bam2Read(b, rf, bam_alt_name); |
| 618 |
> |
} |
| 619 |
> |
else { |
| 620 |
> |
if (!next_fastx_read(*flseqs, rf, read_format, flquals)) { |
| 621 |
> |
r_eof=true; |
| 622 |
> |
break; |
| 623 |
> |
} |
| 624 |
> |
} |
| 625 |
|
uint64_t id = (uint64_t)atol(rf.name.c_str()); |
| 626 |
|
read_pq.push(make_pair(id, rf)); |
| 627 |
|
} |
| 634 |
|
return true; |
| 635 |
|
} |
| 636 |
|
|
| 637 |
+ |
bool ReadStream::get_direct(Read& r, ReadFormat read_format) { |
| 638 |
+ |
if (fstream.file==NULL) return false; |
| 639 |
+ |
if (fstream.is_bam) { |
| 640 |
+ |
if (samread(fstream.bam_file, b) < 0) { |
| 641 |
+ |
r_eof=true; |
| 642 |
+ |
return false; |
| 643 |
+ |
} |
| 644 |
+ |
bam2Read(b, r, bam_alt_name); |
| 645 |
+ |
return true; |
| 646 |
+ |
} |
| 647 |
+ |
if (!next_fastx_read(*flseqs, r, read_format, flquals)) { |
| 648 |
+ |
r_eof=true; |
| 649 |
+ |
return false; |
| 650 |
+ |
} |
| 651 |
+ |
return true; |
| 652 |
+ |
} |
| 653 |
+ |
|
| 654 |
|
// reads must ALWAYS requested in increasing order of their ID |
| 655 |
|
bool ReadStream::getRead(uint64_t r_id, |
| 656 |
|
Read& read, |
| 704 |
|
} //while reads |
| 705 |
|
return found; |
| 706 |
|
} |
| 672 |
– |
|
| 673 |
– |
|
| 674 |
– |
bool get_read_from_stream(uint64_t insert_id, |
| 675 |
– |
FLineReader& fr, |
| 676 |
– |
ReadFormat reads_format, |
| 677 |
– |
bool strip_slash, |
| 678 |
– |
Read& read, |
| 679 |
– |
FILE* um_out, |
| 680 |
– |
bool um_write_found) |
| 681 |
– |
{ |
| 682 |
– |
bool found=false; |
| 683 |
– |
while(!found && !fr.isEof()) |
| 684 |
– |
{ |
| 685 |
– |
read.clear(); |
| 686 |
– |
|
| 687 |
– |
// Get the next read from the file |
| 688 |
– |
if (!next_fastx_read(fr, read, reads_format)) |
| 689 |
– |
break; |
| 690 |
– |
if (strip_slash) |
| 691 |
– |
{ |
| 692 |
– |
string::size_type slash = read.name.rfind("/"); |
| 693 |
– |
if (slash != string::npos) |
| 694 |
– |
read.name.resize(slash); |
| 695 |
– |
} |
| 696 |
– |
uint64_t id = (uint64_t)atoi(read.name.c_str()); |
| 697 |
– |
if (id == insert_id) |
| 698 |
– |
{ |
| 699 |
– |
found=true; |
| 700 |
– |
} |
| 701 |
– |
else if (id > insert_id) |
| 702 |
– |
{ |
| 703 |
– |
fr.pushBack_read(); |
| 704 |
– |
break; |
| 705 |
– |
} |
| 706 |
– |
|
| 707 |
– |
if (um_out && ((um_write_found && found) || |
| 708 |
– |
(!um_write_found && !found))) { |
| 709 |
– |
//write unmapped reads |
| 710 |
– |
fprintf(um_out, "@%s\n%s\n+\n%s\n", read.alt_name.c_str(), |
| 711 |
– |
read.seq.c_str(), read.qual.c_str()); |
| 712 |
– |
} |
| 713 |
– |
//rt.get_id(read.name, ref_str); |
| 714 |
– |
} //while reads |
| 715 |
– |
return found; |
| 716 |
– |
} |
