--d4 missing from v0.3.11 from conda #251
Description
Seems like the d4 option is not available on v0.3.11 downloaded from conda.
❯ mosdepth --help
mosdepth 0.3.11
Usage: mosdepth [options] <prefix> <BAM-or-CRAM>
Arguments:
<prefix> outputs: `{prefix}.mosdepth.global.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).
-a --fragment-mode count the coverage of the full fragment including the full insert (proper pairs only).
-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]
-l --min-frag-len <min-frag-len> minimum insert size. reads with a smaller insert size than this are ignored [default: -1]
-u --max-frag-len <max-frag-len> maximum insert size. reads with a larger insert size than this are ignored. [default: -1]
-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
❯ mosdepth --d4 bams/ERR12115498 bams/ERR12115498.bam
Usage: mosdepth [options] <prefix> <BAM-or-CRAM>
error parsing arguments