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biWFA it #288

Merged
merged 32 commits into from
Oct 30, 2024
Merged

biWFA it #288

merged 32 commits into from
Oct 30, 2024

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ekg
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@ekg ekg commented Oct 28, 2024

Use biWFA all the time.

ekg added 25 commits October 25, 2024 15:22
@ekg
Here is the one-line commit message for the changes:
95c8014 
feat: Add biWFA as default alignment approach with wflign as fallback
@ekg
feat: Add biWFA alignment logic to wflign.cpp
3ffcab8
@ekg
fix: Move wfa_convex_penalties declaration earlier
d576563
@ekg
fix: Move wfa_convex_penalties definition earlier
b9c2727
@ekg
fix: move wfa_convex_penalties definition before first use
ba3f458
@ekg
fix: Set penalties for wfa convex in wflign.cpp
00b27a1
@ekg
fix: Remove duplicate declaration of wfa_convex_penalties
3307042
@ekg
fix: move declaration of wfa_convex_penalties before first use
ec4b7b9
@ekg
okify the declaration of convex penalties
1bafd4e
@ekg
fix: Add missing do_biwfa_alignment() function implementation
1ba06a3
@ekg
fix: Replace write_sam_alignment with write_merged_alignment
4278901
@ekg
fix: feat: Replace write_sam_alignment with `write_merged_alignment…
ed9b5ab 
…` and adapt parameters
@ekg
fix: reverse logic to make biWFA the default aligner
c11e239
@ekg
feat: Add option to force WFLign alignment
69a2631
@ekg
feat: Add force_wflign variable to WFlign class
9602bfd
@ekg
feat: Add force_wflign parameter to align::Parameters struct
beedda8
@ekg
fix: fix incorrect logic for choosing between WFlign and biWFA
78154a3
@ekg
fix: Correct the logic for force_wflign in wflign.cpp
da5aa07
@ekg
line
75d52f8
@ekg
match asm20/defaults for mm2 in biwfa params
bf6f63b
@ekg
fix: Set default chain gap to 2k
92660ca
@ekg
feat: update help text for chain-gap default value
a14e4b4
@ekg
fix: Properly manage alignment_t objects in wflign
f8d9fa9
@ekg
fix: Dereference alignment_t pointer before passing to write_alignmen…
907a16e 
…t_paf
@ekg
fix: Use biWFA for smaller sequences or very high identity matches
263321c
@ASLeonard ASLeonard mentioned this pull request Oct 29, 2024
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@ekg ekg merged commit b160f53 into main Oct 30, 2024
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@ekg