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Smooth chain #272

Merged
merged 29 commits into from
Sep 20, 2024
Merged

Smooth chain #272

merged 29 commits into from
Sep 20, 2024

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ekg
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@ekg ekg commented Sep 14, 2024

More rectifying problems with chaining and mapping splitting.

ekg added 29 commits September 12, 2024 14:40
@ekg
make the direction hard cutoff in chaining more correct
9740f8f
@ekg
more stringent query based sort
41e84af
@ekg
feat: Implement new chaining logic for mapping merging
d7ca6aa
@ekg
feat: Apply chaining logic to second mapping and sort chain pairs in …
09242d8 
…ascending order
@ekg
feat: Modify mergeMappingsInRange function to improve merging logic
869da99
@ekg
simplify sorting and just keep best chain pair option around
68c9df1
@ekg
get rid of axis weighted distance
0e8bcc9
@ekg
comment cleanup
fefb4ee
@ekg
refactor: processChainWithSplits
377f0c5
@ekg
cleanup decision to chain
810ce0a
@ekg
best-buddy chain merging
cb94726
@ekg
feat: Implement filtering based on maximally merged chains
d33a392
@ekg
feat: Restructure mapping and filtering logic
6401eba
@ekg
feat: add filterNonMergedMappings function
29ceaa2
@ekg
one codepath for mapping chain processing
90fe5b6
@ekg
remove unused block coordinate info
c7c171e
@ekg
simplify maximally merged filter
972222d
@ekg
fix: Modify FASTA file mapping to allow self-mapping
99b6681
@ekg
feat: Implement improved mapping merging and filtering
0222496
@ekg
fix: Update distance calculation in range merging to account for stra…
c4408b7 
…nd direction
@ekg
refactor: Improve distance calculation logic in computeMap.hpp
5fb526e
@ekg
refactor: Ensure all fields in merged mappings are properly initialized
c3e2b02
@ekg
feat: Instrument the Lee plane sweep filter algorithm
c89f1b0
@ekg
feat: Add detailed mapping information to debug statements
c67c73b
@ekg
fix: Recalculate blockNucIdentity and handle edge cases in score calc…
7c14341 
…ulation
@ekg
fix: Remove debug statements from liFilterAlgorithm
60ba144
@ekg
fix: Remove debug statements from markGood function
9bdef53
@ekg
fix: Correct calculation of query_end and target_end in tail patching
cd0542e
@ekg
add pafcheck to validation
240a0d3
@ekg ekg merged commit b731e41 into main Sep 20, 2024
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@ekg