Added `--sampleName` and `--readGroup` options to `Bowtie2.align`. Added `--id` and `--idLambda` options to `make-consensus.py` to make it possible to set (or adjust) the name of the generated consensus.
3.1.46
Not secure
Trivial change to setting of `tempdir` in `run-bowtie2.py`.
3.1.45
Not secure
Change call to samtools.
3.1.44
Not secure
Added `--tempdir` argument to `run-bowtie2.py`.
3.1.43
Not secure
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.