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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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Fixed tmpdir for sambamba merge #371

Closed ckuenne closed 5 years ago

ckuenne commented 5 years ago

Hi,

sambamba: 0.6.8

sambamba merge -t 16 union.bam Scr-AtSt_1.bam ... [lots of large bams here]

Sambamba crashed on me when I tried to merge 30GB worth of BAM files, because it filled the /tmp/ folder until there was no space left. I noticed that many other subcommands (e.g. sambamba sort) allow to reset the temporary folder, which would solve this issue for me. So it would be really great if you could implement the "--tmpdir" parameter also for sambamba merge.

Best

mschilli87 commented 5 years ago

@ckuenne: I didn't check but you could try setting TMPDIR to see if it is sufficient to relocate sambamba merge's temporary directory.

ckuenne commented 5 years ago

Yup, that worked. Thanks!