In `reads.py`, changed the `_makeComplementTable` function so that uppercase and lowercase bases are correctly reverse complemented into their respective uppercase and lowercase complementary letters. Added a test to `test/reads.py` to confirm that `reverseComplement` does this.
3.0.59
Not secure
Added `--sampleName` option to `proteins-to-pathogens`.
3.0.58
Not secure
Added `--maxORFLength` option to `extract-ORFs.py`. Fixed logic in retrospect.
3.0.57
Not secure
Added `--removeIds` option to `fasta-diff.sh` (and its helper script `fasta-join.py`).
3.0.56
Not secure
Make `convert-diamond-to-sam.py` print the correct (nucleotide) offset of the start of the match, as though its subject sequence had been nucleotides.
3.0.55
Not secure
Make `convert-diamond-to-sam.py` print the list of required fields in case an input line cannot be split into the expected number of fields.