Added `--showAmbiguous` to `compare-sequences.py`. Pass `--iupac-codes` to `bcftools consensus` in `make-consensus.py`. Add `--max-depth 5000` to `bcftools mpileup` call, also in `make-consensus.py`.
3.1.52
Not secure
Make `sam-coverage-depth.py` not throw an error if there is no coverage at all.
3.1.51
Not secure
Pass the reference id to the `idLambda` function in `make-consensus.py`.
3.1.50
Not secure
Moved `tempdir` assignment in `make-consensus.py` out one level so that it happens including when we are given a VCF file.
3.1.49
Not secure
Wrapped reads saving in a `Reads()` instance in `compare-sequences.py`.