Fix KeyError

[dylanpilz]

Fixes #172

• Drop keys in co_muts that are missing in co_muts_max_reads
• Remove y-ticks from plot-covariants

[dylanpilz]

Instead of dropping keys, fix coverage ranges

• Originally, coverage_end was calculated by coverage_start + len(seq), which runs into issues when there are deletions present, which shorten the length of seq, despite those sites being present in the reference.
• As a result, some mutations towards the end of a read would be out-of-bounds, resulting in reads containing that cluster of mutations to not count to co_muts_max_reads, which in turn results in a KeyError.

• Now uses pysam.AlignedSegment.get_reference_end

  Fix extract definition in _cli.py

• Forgot to update cli definition for extract in #173, which drops --refname argument