Dark-matter

Latest version: v5.0.31

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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.

3.0.54

Not secure
`convert-diamond-to-sam.py` was putting the incorrect (AA, not nucleotide)
reference length into the SAM output. Introduced some spaces for easier
table layout into the HTML generated by `fasta-identity-table.py` when
called by `compare-consensuses.py`.

3.0.53

Not secure
Fixed [650](https://github.com/acorg/dark-matter/issues/650),
exception in `SAMFilter` when quality is `*` in a SAM file.

3.0.52

Not secure
Added hard-clipping to CIGAR in SAM created by `convert-diamond-to-sam.py`.

3.0.51

Not secure
Use `from six import StringIO` to avoid a PY2/3 incompatibility.

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