Added `make-consensus.py` script and tests (for a new `dark/bowtie2.py` file). Upgraded `run-bowtie2.py`.
3.1.42
Not secure
Added `--picard` to `run-bowtie2.py` command to allow removal of duplicates found by Picard.
3.1.41
Not secure
Added `run-bowtie2.py` command.
3.1.40
Not secure
Make `compare-sequences.py` fall back to use `stretcher` if the call to `needle` fails because the sequences are too long.
3.1.39
Not secure
Fixed incorrect calculation of covered offset and total bases counts when excluding reads based on minimum number of overlapping offsets in `dark/genomes.py`.
3.1.38
Not secure
Fix problem with bash set -u checking in `download-genbank.sh`.