Open isthisthat opened 5 years ago
Oucht. Thanks for reporting. I'll try and replicate.
Might be related to this:
sambamba depth base -L chr22_KI270731v1_random:0-150754
gives
sambamba-depth: Conversion negative overflow
but this works:
sambamba depth base -L chr22_KI270731v1_random
same for any contig, I just chose a small one
Can you try the latest release https://github.com/biod/sambamba/releases
closing this for lack of reply.
Hi @pjotrp , sorry for the lack of response! This is still an issue (on my hands at least) with 0.7.1:
sambamba depth base -L chr22_KI270731v1_random:0-150754 NA12878-xxx.bam sambamba 0.7.1 by Artem Tarasov and Pjotr Prins (C) 2012-2019 LDC 1.17.0 / DMD v2.087.1 / LLVM8.0.1 / bootstrap LDC - the LLVM D compiler (1.17.0) REF POS COV A C G T DEL REFSKIP SAMPLE sambamba-depth: Conversion negative overflow
OK, I'll reopen. If it happens with any BAM file it should be easy to reproduce.
Can you send me (a section of) that input file so I can easily replicate the issue?
Ok I've narrowed down the bug. It seems to occur when the start coordinate is zero, e.g.:
sambamba-0.8.0-linux-amd64-static depth base -L chr1:0-10 any.bam
same for region
I'm guessing it uses 1-based coordinates for the chr:start-end definition (as it should).
It seems like a minor thing then.
Great. I can reproduce the issue
./bin/sambamba-0.8.0 depth base -L chr1:0-10 test/issue_204.bam
sambamba 0.8.0
by Artem Tarasov and Pjotr Prins (C) 2012-2020
LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)
REF POS COV A C G T DEL REFSKIP SAMPLE
sambamba-depth: Conversion negative overflow
I love reproducible bugs!
I'm trying to chain a region generator to sambamba depth but it fails or core dups using any of:
but not
Thought I might report since it took ages to debug. Using the latest release (v7). Thanks