Feature Request: allow tmpdir specification

[JohnUrban]

Hi all,

Thanks for the great program. Super easy to use. Seriously.

I ran into a problem with a large BAM file.

panic: write /tmp/smoove-mosdepth-bam175073159: no space left on device

goroutine 11151 [running]:
github.com/brentp/smoove/lumpy.check(...)
    /home/brentp/src/smoove/lumpy/lumpy.go:54
github.com/brentp/smoove/lumpy.remove_sketchy(0xc000030340, 0x33, 0x3e8, 0x7fffaace6523, 0x53, 0x0, 0x0, 0xc000189900, 0x4, 0x4, ...)
    /home/brentp/src/smoove/lumpy/depthfilter.go:323 +0x17dd
github.com/brentp/smoove/lumpy.remove_sketchy_all.func1(0xc00013a5a0, 0x3e8, 0x7fffaace6523, 0x53, 0x0, 0x0, 0xc000189900, 0x4, 0x4, 0x1, ...)
    /home/brentp/src/smoove/lumpy/depthfilter.go:399 +0x231
created by github.com/brentp/smoove/lumpy.remove_sketchy_all
    /home/brentp/src/smoove/lumpy/depthfilter.go:397 +0x194

I've seen this kind of error before with other software/programs on the cluster I'm using. Specifically:

panic: write /tmp/smoove-mosdepth-bam175073159: no space left on device

Apparently this is because the IT in charge of maintaining the cluster has allotted very little space to /tmp.

Sometimes programs have an option like --tmpdir that allows the user to specify a directory explicitly for tmp files. Tjhat would probably solve my issue here.

If you see a work-around, please let me know. The obvious one would be use a different system. Let's pretend that's not possible at the moment.

Thanks for reading.

Best,

John

[brentp]

Hi John, you can use, for example,

export TMPDIR=/somewhere/else/
smoove ...

[JohnUrban]

Well don't I feel silly.

Thanks for the tip!

Closing.