Replace use of `features` in `sam-coverage-depth.py` with the SAM file reference length, to avoid trying to use an undefined `features` variable when no reference is given.
4.0.52
Added `--force` option to `bcftools index` command in `dark/bowtie2.py`.
4.0.51
Added `--reverse` and `--complement` options to `bin/fasta-find.py` to tell it to also look for simple inversions and complement sequences.
4.0.50
Added `bin/fasta-find.py` which, like `bin/fasta-match-offsets.py`, also reports matching sequence offsets in FASTA files but can match numeric regions and also look for reverse complemented matches.
4.0.49
Added `bin/fasta-match-offsets.py` to print offsets of sequence regular expression matches.
4.0.48
More careful calling of `pysam.pileup` in `sam-coverage-depth.py` to avoid an index error if a read mapping extends beyond the end of the reference genome. `pysam` was returning an invalid `column.reference_pos` in that case (invalid because the value is beyond the end of the reference, so it can't be used as a reference offset).