Location of temp files for -r

hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes

MIT License

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Location of temp files for -r #71

Open tseemann opened 3 years ago

tseemann commented 3 years ago

I notice when using -r that the temporary files are created in the current direcrtory

eg.

qqenkendpy.bwt
qqenkendpy.pac
qqenkendpy.ann
qqenkendpy.amb

Can you pleae use the system temddir*() function? Normallt that would use /tmp or $TMPDIR set by the user or system.

hsinnan75 commented 3 years ago

Yes, they are kept after the whole process terminates, so that users can use the index files for next run. If it is not good, I'll consider to remove them when the process finishes.

tseemann commented 3 years ago

Because they have random names, how will the user know where or what they are?

They should use the PODIX temp file functions and be deleted at the end.

These functions are probably in C++ std ?