Repetitive read count fix

[agshumate]

We observed some cases where the number of repetitive reads was exceeding the number of total reads. This is due to counting repetitive reads at the locus level rather than the marker level. This PR fixes that issue and refactors some code to make the logic more clear.

---

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

[agshumate]

Confirmed that these changes fix the issue on a full-sized set of reads.