sambamba depth output coordinate system

[tahuh]

Hi

I am using sambamba version 0.7.0 and 0.7.1

I have tested the depth format to count up the bases with command below

sambamba depth base -L chr7:55191822-55191823 in.bam

0.7.0 produce as shown below

sambamba 0.7.0
 by Artem Tarasov and Pjotr Prins (C) 2012-2019
    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
Processing reference #7 (chr7)
chr7    55191821    1819236 470 540 7888    1810336 1   0   sample
chr7    55191822    1820067 928 68  1818295 694 82  0   sample

0.7.1 shows

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
Processing reference #7 (chr7)
chr7    55191821    1819236 470 540 7888    1810336 1   0   sample
chr7    55191822    1820067 928 68  1818295 694 82  0   sample

Is sambamba designed to flush output in zero based context or is this problem is a bug?

Thanks

[pjotrp]

If you search for https://github.com/biod/sambamba/issues?q=is%3Aissue+zero you'll find more.

[tahuh]

Hi @pjotrp I found the answer via link you have attatched (link : https://github.com/biod/sambamba/issues/293)

Now I think it is okay to close this issue. Thanks!