| 600 |
|
//only needed for the primary input files (given by user) |
| 601 |
|
string picmd(""); |
| 602 |
|
string fext=getFext(fname); |
| 603 |
+ |
if (fext=="bam") { |
| 604 |
+ |
picmd="bam2fastx"; |
| 605 |
+ |
return picmd; |
| 606 |
+ |
} |
| 607 |
|
if (fext=="gz" || fext=="gzip" || fext=="z") { |
| 608 |
|
if (use_all_cpus && str_endsWith(zpacker,"pigz")) { |
| 609 |
|
picmd=zpacker; |
| 652 |
|
} |
| 653 |
|
|
| 654 |
|
string getUnpackCmd(const string& fname, bool use_all_cpus) { |
| 655 |
< |
//prep_reads should use guess_packer() instead |
| 655 |
> |
//prep_reads should use guess_packer() instead |
| 656 |
|
string pipecmd(""); |
| 657 |
< |
if (zpacker.empty() || getFext(fname)!="z") { |
| 657 |
> |
string fext=getFext(fname); |
| 658 |
> |
if (fext=="bam") { |
| 659 |
> |
pipecmd="bam2fastx"; |
| 660 |
> |
return pipecmd; |
| 661 |
> |
} |
| 662 |
> |
if (zpacker.empty() || fext!="z") { |
| 663 |
|
return pipecmd; |
| 664 |
|
} |
| 665 |
|
pipecmd=zpacker; |
