[codex] Merge overlapping fragment mates during assembly

[iskandr]

Summary

• conservatively merge overlapping paired-end reads from the same fragment when run_isovar builds read evidence for assembly
• preserve raw read counts with source_read_count so count fields and adapter evidence stay numerically correct
• keep raw read and CLI surfaces unchanged by making fragment merging opt-in on ReadCollector
• add regressions for the merged fragment sequence and preserved raw read counts
• bump isovar to 1.5.1

Why

Issue #59 asks Isovar to stop treating overlapping mate pairs as independent evidence when assembling cDNA around a variant. That duplicated overlap can fragment assembly and overstate support in downstream assembled-sequence metrics.

Validation

• ./lint.sh
• ./test.sh

Closes #59

[coveralls]

coverage: 93.113% (-0.2%) from 93.305% — codex/merge-overlapping-fragments into master