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@brentp brentp released this 09 Oct 18:08
v0.1.9
db841f8

This is a breaking release. A given output will be unchanged, but the command-line usage to get it will be different. I apologize for the change in use, but not for the increase in utility. In order to expose the utility of mosdepth across more (and multiple simultaneous) uses, mosdepth now requires a prefix for outputs rather than sending it to stdout. Usage as of this release looks as below. Where previous usage was e.g.

mosdepth $bam > $output

current usage becomes:

mosdepth $output_prefix $bam

This is explained in more detail in the help:

mosdepth 0.1.9

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

Arguments:

  <prefix>       outputs: `{prefix}.mosdepth.dist.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)

  <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).
  -f --fasta <fasta>         fasta file for use with CRAM files.

Other options:

  -F --flag <FLAG>            exclude reads with any of the bits in FLAG set [default: 1796]
  -q --quantize <segments>    write quantized output, see docs for description.
  -Q --mapq <mapq>            mapping quality threshold [default: 0]
  -h --help                   show help
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