Eric Coissac e511650f5b Refactor similarity engine and implement parallel clustering ...

Introduces parallel processing for clustering, refines scoring mechanisms, and expands test coverage for the alignment functionality.

This change introduces parallel processing capabilities within the clustering logic, updates the core similarity engine with new data structures and scoring methods, and implements a comprehensive test suite for the alignment tool. It also adds new command-line options for configuring alignment parameters and reference lengths.

2026-11-03 14:04:32 +11:00

..

alignment.go

Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

2025-03-25 16:44:46 +01:00

backtracking.go

EndGapFree alignments

2024-09-24 15:52:12 +02:00

dnamatrix.go

Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

2025-03-25 16:44:46 +01:00

fastlcs_bench_test.go

Implement Banded LCS calculation with scalar and SIMD support

2026-11-03 09:28:46 +11:00

fastlcs.go

add the --min-sample-count option to obiclean.

2025-02-24 08:48:31 +01:00

fastlcsegf.go

Implement Banded LCS calculation with scalar and SIMD support

2026-11-03 09:28:46 +11:00

fourbitsencode.go

Change path of the obitools pkg

2023-11-29 12:14:37 +01:00

is_d0_or_d1.go

Correction on obiformat of bug leading to partial parsing and add godocs

2024-05-07 10:54:12 +02:00

lcsband_nosimd.go

Implement core clustering logic and scoring features

2026-11-03 09:32:40 +11:00

lcsband_scalar.go

Implement Banded LCS calculation with scalar and SIMD support

2026-11-03 09:28:46 +11:00

lcsband_simd.go

Implement Banded LCS calculation with scalar and SIMD support

2026-11-03 09:28:46 +11:00

lcsband_test.go

Implement core clustering logic and scoring features

2026-11-03 09:32:40 +11:00

lcsband.go

Implement core clustering logic and scoring features

2026-11-03 09:32:40 +11:00

lcsmin.go

Refactor similarity engine and implement parallel clustering

2026-11-03 14:04:32 +11:00

lcsscore_simd.go

Implement core clustering logic and scoring features

2026-11-03 09:32:40 +11:00

locatepattern_test.go

fix: validate inputs and fix coordinate offsets in pattern matching

2026-08-19 17:25:44 +02:00

locatepattern.go

fix: validate inputs and fix coordinate offsets in pattern matching

2026-08-19 17:25:44 +02:00

pairedendalign.go

Changes to be committed:

2025-02-23 17:37:56 +01:00

readalign.go

Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

2025-03-25 16:44:46 +01:00