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).
4.0.47
Added printing of transversion and transition counts to `bin/codon-distance.py`. Output is sorted first by distance, then by number of transitions (highest to lowest) then by codon DNA. The idea being to present the possible codon changes to get from one amino acid to another in the order that requires the least change to the most.
The lists in the values in the dict returned by `codonInformation` now contain 2-tuples instead of lists of length 2. If you pass `countTransitions=True` to that function it will also put the count of the number of transitions (as opposed to transversions) into the tuple. See the tests in `test/test_codonDistance.py`.
4.0.46
Added `--reference` option to `sam-coverage-depth.py`.