[codex] Left-align equivalent indels

[iskandr]

Summary

This PR teaches ReadCollector to left-align equivalent indels within a read alignment so that homopolymer insertions/deletions are counted against the queried canonical variant instead of being treated as reference support.

What changed

• detect insertion and deletion events from pysam aligned pairs when a specific variant is being queried
• walk each equivalent one-base-left-shift state inside the local alignment and match it against the queried trimmed variant
• rewrite the logical read interval to the canonical left-aligned indel split when a match is found
• relax AlleleRead.from_locus_read(...) so it trusts the collector's logical interval for canonicalized insertions
• add locus-read and read-evidence regressions for right-shifted homopolymer insertions and deletions
• bump isovar to 1.4.23

Why

Issue #79 is a correctness bug: DNA variants are generally left-aligned, but RNA aligners may place an equivalent indel later within a repeat. Isovar previously compared only the literal allele at the queried locus, so those equivalent alignments were counted as ref/other instead of alt.

Impact

• equivalent homopolymer indels now collapse onto the same canonical variant locus
• downstream allele read exports and read counts become stable across alignment placement of the same indel
• the assembly layer now sees a consistent logical indel split for those reads

Validation

• ./lint.sh
• ./test.sh

Closes #79

[coveralls]

coverage: 93.4% (-0.04%) from 93.441% — fix-left-align-indels into master