Implement fragments aggregation into instances: modified main.py and map.py

[marco-cominelli01]

Edit --locus flag to --locus-level [disabled, fragment, instance] to choose between subfamily level, using individual repeats fragments as locus or grouping fragments to repeats instances (bona fide insertions)

[Copilot]

Pull request overview

This pull request implements a new feature for aggregating repeat fragments into instances, replacing the boolean --locus flag with a string-valued --locus-level flag that supports three modes: disabled (subfamily-level quantification), fragment (individual repeat fragments as loci), and instance (grouped fragments representing bona fide insertions).

Changes:

• Modified the command-line interface to use --locus-level [disabled, fragment, instance] instead of --locus boolean flag
• Implemented instance aggregation logic in map.py that groups repeat fragments by their RepeatMasker instance ID
• Updated the rmsk.bed.gz file format to use RepeatMasker instance IDs instead of sequential locus indices

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.

File	Description
irescue/main.py	Updated argument parser to use --locus-level with string choices instead of boolean --locus flag, updated references from args.locus to args.locus_level
irescue/map.py	Modified makeRmsk() and chrcat() functions to accept string locus parameter; implemented instance aggregation logic that creates an rmsk_instance.bed.gz file with merged instance metadata; changed rmsk.bed.gz 5th column from sequential index to instance ID
tests/test.yml	Updated test commands to use new --locus-level flag syntax, added new test case for instance mode, updated md5sum checksums to reflect file format changes

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