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; |