samtools/samtools — pull request #321 by peterjc (2014-11-19 17:45:11+00:00)
Title: Replace 'samtools depth' cryptic 'minQLen' with real description

Could anyone understand 'minQLen' in the 'samtools depth' help?

```
$ ./samtools depth

Usage: samtools depth [options] in1.bam [in2.bam [...]]
Options:
-b list of positions or regions
-f

list of input BAM filenames, one per line [null]
-l minQLen
-q base quality threshold
-Q mapping quality threshold
-r region
```

Reading the source code, this is mapped to variable ``min_len`` which (if set) is compared to each mapped read's length calculated from the CIGAR string using ``bam_cigar2qlen(b->core.n_cigar, bam_get_cigar(b))``.

I think it makes more sense to label the ``-l`` option as "minimum mapped read length (from CIGAR string)" as per this one-line change.