New alerts in final report

[standage]

In #183, MicroHapulator was updated to mark gap alleles as - instead of leaving them empty, causing the read to be discarded. This allows the user to distinguish between SNPs that are not covered by the read and SNPs that are covered by the read but have an alignment gap. The prevalence of reads with gaps can elucidate the presence of indel variants.

In this PR, two new tables are added to report potentially problematic markers. Table 4.3 shows markers that have a high proportion of aligned reads (default >25%) that don't span all SNPs. Table 4.4 shows markers with a high proportion of reads (default >5%) containing alignment gaps. The presence of either such artifact is important for troubleshooting the success of a sequencing run and the analysis and interpretation of a typing result.

Closes #184.

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• Changes are clearly described above
• Any relevant issue threads are referenced in the description
• Any new features are tested (see the development manual for details)
• CLI documentation (see docs/cli.md) and Python API documentation (see microhapulator/api.py) are up-to-date and in sync
• Substantial changes are documented in CHANGELOG.md (see https://keepachangelog.com/en/1.0.0/)