| 173 |
|
|
| 174 |
|
bool next_fastx_read(FLineReader& fr, Read& read, ReadFormat reads_format, |
| 175 |
|
FLineReader* frq) { |
| 176 |
+ |
if (fr.pushed_read) |
| 177 |
+ |
{ |
| 178 |
+ |
read = fr.last_read; |
| 179 |
+ |
fr.pushed_read = false; |
| 180 |
+ |
return true; |
| 181 |
+ |
} |
| 182 |
+ |
|
| 183 |
|
read.clear(); |
| 184 |
|
char* buf=NULL; |
| 185 |
|
while ((buf=fr.nextLine())!=NULL) { |
| 261 |
|
return false; |
| 262 |
|
} |
| 263 |
|
} |
| 264 |
+ |
|
| 265 |
+ |
fr.last_read = read; |
| 266 |
|
return !(read.seq.empty()); |
| 267 |
|
} |
| 268 |
|
|
| 618 |
|
|
| 619 |
|
// reads must ALWAYS requested in increasing order of their ID |
| 620 |
|
bool ReadStream::getRead(uint64_t r_id, |
| 621 |
< |
Read& read, |
| 622 |
< |
ReadFormat read_format, |
| 623 |
< |
bool strip_slash, |
| 624 |
< |
FILE* um_out, //unmapped reads output |
| 625 |
< |
bool um_write_found) { |
| 621 |
> |
Read& read, |
| 622 |
> |
ReadFormat read_format, |
| 623 |
> |
bool strip_slash, |
| 624 |
> |
FILE* um_out, //unmapped reads output |
| 625 |
> |
bool um_write_found, |
| 626 |
> |
uint64_t begin_id, |
| 627 |
> |
uint64_t end_id) { |
| 628 |
|
if (!fstream.file) |
| 629 |
|
err_die("Error: calling ReadStream::getRead() with no file handle!"); |
| 630 |
|
if (r_id<last_id) |
| 636 |
|
// Get the next read from the file |
| 637 |
|
if (!next_read(read, read_format)) |
| 638 |
|
break; |
| 639 |
+ |
|
| 640 |
|
if (strip_slash) { |
| 641 |
|
string::size_type slash = read.name.rfind("/"); |
| 642 |
|
if (slash != string::npos) |
| 643 |
|
read.name.resize(slash); |
| 644 |
|
} |
| 645 |
< |
if ((uint64_t)atoi(read.name.c_str()) == r_id) { |
| 646 |
< |
found=true; |
| 647 |
< |
} |
| 636 |
< |
if (um_out && (um_write_found || !found)) { |
| 637 |
< |
//write unmapped reads |
| 638 |
< |
fprintf(um_out, "@%s\n%s\n+\n%s\n", read.alt_name.c_str(), |
| 639 |
< |
read.seq.c_str(), read.qual.c_str()); |
| 640 |
< |
} |
| 641 |
< |
//rt.get_id(read.name, ref_str); |
| 642 |
< |
} //while reads |
| 643 |
< |
return found; |
| 644 |
< |
} |
| 645 |
> |
uint64_t id = (uint64_t)atol(read.name.c_str()); |
| 646 |
> |
if (id >= end_id) |
| 647 |
> |
return false; |
| 648 |
|
|
| 649 |
+ |
if (id < begin_id) |
| 650 |
+ |
continue; |
| 651 |
|
|
| 652 |
< |
bool get_read_from_stream(uint64_t insert_id, |
| 648 |
< |
FILE* reads_file, |
| 649 |
< |
ReadFormat reads_format, |
| 650 |
< |
bool strip_slash, |
| 651 |
< |
Read& read, |
| 652 |
< |
FILE* um_out, |
| 653 |
< |
bool um_write_found |
| 654 |
< |
) { |
| 655 |
< |
FLineReader fr(reads_file); |
| 656 |
< |
bool found=false; |
| 657 |
< |
while(!found && !fr.isEof()) |
| 658 |
< |
{ |
| 659 |
< |
read.clear(); |
| 660 |
< |
// Get the next read from the file |
| 661 |
< |
if (!next_fastx_read(fr, read, reads_format)) |
| 662 |
< |
break; |
| 663 |
< |
if (strip_slash) |
| 652 |
> |
if (id == r_id) |
| 653 |
|
{ |
| 654 |
< |
string::size_type slash = read.name.rfind("/"); |
| 666 |
< |
if (slash != string::npos) |
| 667 |
< |
read.name.resize(slash); |
| 654 |
> |
found=true; |
| 655 |
|
} |
| 656 |
< |
if ((uint64_t)atoi(read.name.c_str()) == insert_id) |
| 656 |
> |
else if (id > r_id) |
| 657 |
|
{ |
| 658 |
< |
//return true; |
| 659 |
< |
found=true; |
| 658 |
> |
read_pq.push(make_pair(id, read)); |
| 659 |
> |
break; |
| 660 |
|
} |
| 661 |
+ |
|
| 662 |
|
if (um_out && (um_write_found || !found)) { |
| 663 |
|
//write unmapped reads |
| 664 |
|
fprintf(um_out, "@%s\n%s\n+\n%s\n", read.alt_name.c_str(), |
| 665 |
|
read.seq.c_str(), read.qual.c_str()); |
| 666 |
|
} |
| 679 |
– |
//rt.get_id(read.name, ref_str); |
| 667 |
|
} //while reads |
| 668 |
|
return found; |
| 669 |
|
} |
| 670 |
|
|
| 671 |
|
|
| 672 |
|
bool get_read_from_stream(uint64_t insert_id, |
| 673 |
< |
FILE* reads_file, |
| 673 |
> |
FLineReader& fr, |
| 674 |
|
ReadFormat reads_format, |
| 675 |
|
bool strip_slash, |
| 676 |
< |
char read_name [], |
| 677 |
< |
char read_seq [], |
| 678 |
< |
char read_alt_name [], |
| 692 |
< |
char read_qual [], |
| 693 |
< |
FILE* um_out) |
| 676 |
> |
Read& read, |
| 677 |
> |
FILE* um_out, |
| 678 |
> |
bool um_write_found) |
| 679 |
|
{ |
| 680 |
< |
Read read; |
| 681 |
< |
FLineReader fr(reads_file); |
| 697 |
< |
while(!fr.isEof()) |
| 680 |
> |
bool found=false; |
| 681 |
> |
while(!found && !fr.isEof()) |
| 682 |
|
{ |
| 683 |
|
read.clear(); |
| 684 |
|
|
| 685 |
|
// Get the next read from the file |
| 686 |
|
if (!next_fastx_read(fr, read, reads_format)) |
| 687 |
|
break; |
| 704 |
– |
|
| 688 |
|
if (strip_slash) |
| 689 |
|
{ |
| 690 |
|
string::size_type slash = read.name.rfind("/"); |
| 691 |
|
if (slash != string::npos) |
| 692 |
|
read.name.resize(slash); |
| 693 |
|
} |
| 694 |
< |
|
| 695 |
< |
if ((uint64_t)atoi(read.name.c_str()) == insert_id) |
| 694 |
> |
uint64_t read_id = (uint64_t)atoi(read.name.c_str()); |
| 695 |
> |
if (read_id == insert_id) |
| 696 |
> |
{ |
| 697 |
> |
found=true; |
| 698 |
> |
} |
| 699 |
> |
else if (read_id > insert_id) |
| 700 |
|
{ |
| 701 |
< |
if (read_name) strcpy(read_name, read.name.c_str()); |
| 702 |
< |
if (read_seq) strcpy(read_seq, read.seq.c_str()); |
| 716 |
< |
if (read_alt_name) strcpy(read_alt_name, read.alt_name.c_str()); |
| 717 |
< |
if (read_qual) strcpy(read_qual, read.qual.c_str()); |
| 718 |
< |
return true; |
| 701 |
> |
fr.pushBack_read(); |
| 702 |
> |
break; |
| 703 |
|
} |
| 704 |
< |
else if (um_out!=NULL) { |
| 704 |
> |
|
| 705 |
> |
if (um_out && (um_write_found || !found)) { |
| 706 |
|
//write unmapped reads |
| 707 |
< |
fprintf(um_out, "@%s\n%s\n+\n%s\n", read.alt_name.c_str(), read.seq.c_str(), |
| 708 |
< |
read.qual.c_str()); |
| 707 |
> |
fprintf(um_out, "@%s\n%s\n+\n%s\n", read.alt_name.c_str(), |
| 708 |
> |
read.seq.c_str(), read.qual.c_str()); |
| 709 |
|
} |
| 710 |
< |
|
| 726 |
< |
//rt.get_id(read.name, ref_str); |
| 710 |
> |
//rt.get_id(read.name, ref_str); |
| 711 |
|
} //while reads |
| 712 |
< |
|
| 729 |
< |
return false; |
| 712 |
> |
return found; |
| 713 |
|
} |
