mosdepth

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Hi, I wanted to use the --d4 option from the latest version but mosdepth installed through bioconda does not appear to have it.

At first I thought there was an issue with the bioconda recipe, but looking at it the downloaded version and sha sum seems all good.

I did not find where it is going wrong.

mosdepth 0.3.1

  Usage: mosdepth [options] <prefix> <BAM-or-CRAM>

Arguments:

  <prefix>       outputs: `{prefix}.mosdepth.dist.txt`
                          `{prefix}.mosdepth.summary.txt`
                          `{prefix}.per-base.bed.gz` (unless -n/--no-per-base is specified)
                          `{prefix}.regions.bed.gz` (if --by is specified)
                          `{prefix}.quantized.bed.gz` (if --quantize is specified)
                          `{prefix}.thresholds.bed.gz` (if --thresholds is specified)

  <BAM-or-CRAM>  the alignment file for which to calculate depth.

Common Options:

  -t --threads <threads>     number of BAM decompression threads [default: 0]
  -c --chrom <chrom>         chromosome to restrict depth calculation.
  -b --by <bed|window>       optional BED file or (integer) window-sizes.
  -n --no-per-base           dont output per-base depth. skipping this output will speed execution
                             substantially. prefer quantized or thresholded values if possible.
  -f --fasta <fasta>         fasta file for use with CRAM files [default: ].

Other options:

  -F --flag <FLAG>              exclude reads with any of the bits in FLAG set [default: 1796]
  -i --include-flag <FLAG>      only include reads with any of the bits in FLAG set. default is unset. [default: 0]
  -x --fast-mode                dont look at internal cigar operations or correct mate overlaps (recommended for most use-cases).
  -q --quantize <segments>      write quantized output see docs for description.
  -Q --mapq <mapq>              mapping quality threshold. reads with a quality less than this value are ignored [default: 0]
  -T --thresholds <thresholds>  for each interval in --by, write number of bases covered by at
                                least threshold bases. Specify multiple integer values separated
                                by ','.
  -m --use-median               output median of each region (in --by) instead of mean.
  -R --read-groups <string>     only calculate depth for these comma-separated read groups IDs.
  -h --help                     show help

It seems that the bioconda compilation was done without d4 support.

1. First you must install d4 (https://github.com/38/d4-format). Clone the repo, enter the directory "d4bindings" and follow the "install.sh" script or fix the paths to your convenience: cargo-build and copy the two files (d4bindings/include/d4.h and the newly created target/release/libd4binding.so). For me it is /usr/include and /usr/lib64.

2. Clone this package (mosdepth), edit the file "nim.cfg" adding the following two lines "-d:d4" and "-d:danger" to the top of the file.

3. Build and install the package with "nimble install".

4. Run mosdepth with the flag --d4 and without -n|--no-per-base

Thanks, indeed that's what I understood with the compilation that happened on bioconda. I took another route to install d4 in fact, I used the rust package manager cargo to install d4utils. I needed an easy way so that it could be installed inside a singularity container, without the need to modify compiler directives (a bit tricky to do automatically in a container recipe).