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break up main annotation function into small pieces #405

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merged 33 commits into from
Apr 17, 2024
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09ff7a3
Extract annotate_perf_matches_initial.
macklin-10x Mar 20, 2024
d778e6f
Extract the second phase of perfect match-finding.
macklin-10x Mar 20, 2024
50d247f
Couple of tweaks to second phase perfect match.
macklin-10x Mar 20, 2024
a23756d
Extract merge_perfect_matches.
macklin-10x Mar 20, 2024
5fb97ef
Extract extend_matches.
macklin-10x Mar 20, 2024
d062cb9
Extract annotate_40mers_for_mouse_a20
macklin-10x Mar 20, 2024
11f286f
Extract extend_matches_to_end_of_reference
macklin-10x Mar 21, 2024
ff1c4ab
Extract extend_between_match_blocks
macklin-10x Mar 21, 2024
1c19064
Extract merge_overlapping_alignments
macklin-10x Mar 21, 2024
e775016
Extract extend_long_v_gene_alignments
macklin-10x Mar 21, 2024
18d557f
Extract remove_subsumed_alignments
macklin-10x Mar 21, 2024
6de7f84
Extract delete_improper_matches, including the bug.
macklin-10x Mar 21, 2024
deeda43
Fix the confused logic that was previously implemented using mem::swap
macklin-10x Mar 21, 2024
a2d6d5e
Add TODO comments on collapsing the different match types together.
macklin-10x Mar 21, 2024
8f88b9c
Extract remove_inferior_matches
macklin-10x Mar 21, 2024
56b028d
Extract find_indels_in_v_or_utr
macklin-10x Mar 21, 2024
39fb7ad
Extract retain_best_alignment
macklin-10x Mar 21, 2024
412559b
Extract remove_subsumed_alignments and leave a FIXME to collapse them.
macklin-10x Mar 21, 2024
8c5cc82
Extract extend_alignments
macklin-10x Mar 21, 2024
b8a116f
Extract retain_longer_v_alignments
macklin-10x Mar 21, 2024
d9b4a9d
Extract annotate_j_for_ig_with_c_and_v
macklin-10x Mar 21, 2024
2c3ec96
Extract delete_d_if_chain_doesnt_match_v
macklin-10x Mar 21, 2024
96b4e6d
Extract annotate_d_between_v_j
macklin-10x Mar 21, 2024
82ad7c5
Extract retain_longer_j_segment
macklin-10x Mar 21, 2024
fe0c9fe
Extract retain_better_c_segment
macklin-10x Mar 21, 2024
793493e
Extract retain_better_v_segment
macklin-10x Mar 21, 2024
8ec96fa
Extract retain_much_better_aligned_v_segment
macklin-10x Mar 21, 2024
cf1ede9
Extract remove_unmatched_trbc
macklin-10x Mar 21, 2024
aae1598
Extract downselect_equally_performant_j_and_c
macklin-10x Mar 21, 2024
2343eca
Extract downselect_to_best_c
macklin-10x Mar 21, 2024
a0dd8be
Re-use remove_utr_without_matching_v, yay
macklin-10x Mar 21, 2024
a536a50
Extract remove_subsumed_extended_alignments
macklin-10x Mar 21, 2024
16096b7
Remove refdata binding.
macklin-10x Mar 21, 2024
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