markdup tmp file name

[rernst]

Running markdup in paralel (using the same tmp folder for all processes) will result in a crash: sambamba-markdup: Failed to remove file /tmp/sorted.0.bam: No such file or directory.

Can probably be solved by using an unique or random filename?

[pjotrp]

:) I am working on similar things with bio-vcf. I suggest we use $TEMDIR/sambamba-pid5466/sorted.0.bam, instead, where pid is the mother process id. It would be even better to use named random names, but a collision is unlikely using the pid dir and it is much easier to clean up after.

[lomereiter]

Good point, it should be fixed now.
@pjotrp thanks for suggestion, I decided to add both PID and random suffix to subdirectory name.

[rernst]

Awesome, thanks for the very quick fix!