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Tweak hits #292

Merged
merged 28 commits into from
Nov 11, 2024
Merged

Tweak hits #292

merged 28 commits into from
Nov 11, 2024

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ekg
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@ekg ekg commented Nov 9, 2024

Debugging indexing (n.b. current main can drop parts of the index due to badly implement parallel index merging).

Remove entries from the index if they have too many hits, for manual experimentation with mapping runtime in big genomes with big repeats.

Modify "L1" filter pass scan min count of minmer hits in a segment window.

ekg added 28 commits November 8, 2024 10:21
@ekg
feat: Optimize minimum hits calculation with segment length caching
760d7df
@ekg
feat: Add logging of L1 filtering parameters in mapQuery method
f7bb353
@ekg
style: Compact logging of L1 filtering parameters on a single line
a9bc8da
@ekg
fix: Display percent identity as percentage in logging
6d4219c
@ekg
refactor: Simplify logging to only show cached_minimum_hits parameter
22d9a2c
@ekg
feat: Expose minimum hits parameter for L1 filtering in wfmash
6f7a954
@ekg
fix: Correct typo in chain gap parsing and add comment about argument…
9ef3636 
… parsing
@ekg
refactor: Restructure HG filter parsing with comma-separated list and…
75fbd25 
… defaults
@ekg
feat: Add min-hits parameter with auto default for L1 filtering
74f09aa
@ekg
oops typo
dbc0ab0
@ekg
fix: Respect min-hits parameter in L1 filtering logic
aac46fd
@ekg
feat: Add k-mer frequency threshold parameter for mapping
57d721f
@ekg
fix: Capture kmer_freqs in lambda to resolve compilation error
124506e
@ekg
feat: Implement k-mer frequency filtering during index building
cedf4c2
@ekg
fix: Conditionally set lower triangular mapping flag to prevent unint…
d6d1a0b 
…ended default
@ekg
feat: Add logging for k-mer filtering statistics during index building
1febc20
@ekg
refactor: Convert parallel index building to serial implementation
03a2ea7
@ekg
refactor: Optimize k-mer filtering by using position list size instea…
cb5b86f 
…d of frequency counting
@ekg
refactor: Optimize k-mer frequency filtering with single-pass approach
f8b6b1e
@ekg
fix messed up progress problem
9f6783c
@ekg
refactor: Update parameter names for l1-hits and max-kmer-freq with s…
8404f96 
…hort options
@ekg
refactor: Rename --input-mapping to --align-paf and update description
2e65603
@ekg
refactor: Modify k-mer filtering to occur after position list aggrega…
8973d3c 
…tion
@ekg
refactor: Always add to minmer index and clear frequent k-mer positio…
f7a304d 
…n lists
@ekg
always store positions, but may be empty
75e7114
@ekg
refactor: Improve k-mer frequency filtering with two-pass approach
8fb45ce
@ekg
refactor: Replace std::unordered_map with MI_Map_t for k-mer frequenc…
c41dbb1 
…y counting
@ekg
fix: Correct k-mer frequency map type in winSketch
8f18e1f
@ekg ekg merged commit fb42892 into main Nov 11, 2024
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