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.
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