export SMOOVE_MAX_DEPTH=20000 doesn't work

brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.

Apache License 2.0

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export SMOOVE_MAX_DEPTH=20000 doesn't work #242

Closed yqlan closed 2 weeks ago

yqlan commented 2 weeks ago

command: export SMOOVE_MAX_DEPTH=5000 smoove call ...

log file output: [smoove] 2024/06/14 14:20:10 starting with version 0.2.8 [smoove] 2024/06/14 14:20:11 calculating bam stats for 8 bams [smoove] 2024/06/14 14:20:43 done calculating bam stats [smoove] 2024/06/14 14:20:43 couldn't set max depth to 5000

brentp commented 2 weeks ago

oops. the error is in the wrong place. that means it succeeded. I have pushed a fix but you can proceed knowing that it will set the depth as requested.