--d4 Creates d4 files with inf/NaN values #237
Description
Been doing some work in the d4 repo and wanted to compare d4 files made using d4tools create and mosdepth. However with the small BAMs I've been testing with, mosdepth created d4 files have inf/NaN values for depth. Not sure if this is an issue with d4 or mosdepth.
Mosdepth versions tested: 0.3.6 (from conda) and 0.3.8 (the mosdepth_d4 binary in the releases page)
d4tools was built from source in a fresh clone of the repo.
d4tools create
> d4tools create -Azr ../data/genome.fna.fai ../data/test.bam test.d4
> d4tools show test.d4 > show.out
> head show.out
NC_052520.2 0 116790 0
NC_052520.2 116790 116942 1
NC_052520.2 116942 116946 0
NC_052520.2 116946 117093 1
NC_052520.2 117093 138700 0
NC_052520.2 138700 138848 1
NC_052520.2 138848 138852 2
NC_052520.2 138852 139000 1
NC_052520.2 139000 225154 0
NC_052520.2 225154 225306 1
mosdepth 0.3.6
> mosdepth --d4 test ../data/test.bam
> d4tools show test.per-base.d4 > show.out
> head show.out
NC_052520.2 0 36240 NaN
NC_052520.2 36240 36391 inf
NC_052520.2 36391 36426 NaN
NC_052520.2 36426 36577 inf
NC_052520.2 36577 43701 NaN
NC_052520.2 43701 43971 inf
NC_052520.2 43971 116790 NaN
NC_052520.2 116790 116941 inf
NC_052520.2 116941 116946 NaN
NC_052520.2 116946 117092 inf
0.3.8 is the same output as 0.3.6, no need to show it here.
Attached zipped folder of all the files for reference.
mosdepth-test.zip