sambamba depth window sementation fault [core dump] using --combined flag - Githubissues

biod / sambamba

Tools for working with SAM/BAM data

http://thebird.nl/blog/D_Dragon.html

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sambamba depth window sementation fault [core dump] using --combined flag #395

Closed iamh2o closed 5 years ago

iamh2o commented 5 years ago

version of sambamba == 0.6.8
version of samtools if the issue is with pileup tool = N/A
the command line or bash script used (feel free to shorten paths and filenames)

sambamba depth window --combined -w 1000 -c 0 -q=30 -m ./A.bam ./B.bam

Outputs: sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018 LDC 1.13.0 / DMD v2.083.1 / LLVM7.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)

# chrom chromStart chromEnd readCount meanCoverage Processing reference #1 (chr1) chr1 9000 10000 12 0.014 Segmentation fault (core dumped)

The --combined flag is causing the problem here. When it is removed, the tool executes normally.

whenever possible, a set of BAM/BED files to reproduce the issue I am using a 40x coverage WGS NA12878 BAM and a 40x WGS NA24385 BAM. Too large to include. The problem does not present when I test small BAMs however.

pjotrp commented 5 years ago

Can you try 0.6.6 and see if it does the same? May be a duplicate of #394