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Commits on Jun 3, 2024

• Use conditional import for omp.h

  rlorigro

  committed
  1cf38ea

Commits on Apr 20, 2024

• Merge pull request #91 from pjotrp/main

  Show description for cf3eb92
  smarco

  authored
  cf3eb92

• benchmark: disable test when OPENMP is not linked in

  pjotrp

  committed
  86e9de9

Commits on Mar 31, 2024

• Fixed parsing cmdline for ends-free parameters

  smarco

  committed
  49dc9a3

Commits on Sep 30, 2023

• Fixed define (gcc complaining) and label on align-bench

  smarco

  committed
  99a5879

Commits on Sep 25, 2023

• Added extension mode to align_benchmark (for testing)

  smarco

  committed
  d09e0b2

Commits on Aug 10, 2023

• Updated generate_dataset README (resolves #78)

  smarco

  committed
  0c6de10

Commits on Jul 17, 2023

• Changed align_benchmark general global-timer to measure benchmark call (without I/O) to be more informative. Alignment-timer remains the same.

  smarco

  committed
  6dd4298

Commits on Mar 24, 2023

• Base-case alignments on BiWFA respect the direction used to determine the breakpoint

  smarco

  committed
  30a0d79

Commits on Mar 19, 2023

• Fixed bug when biwfa using heuristics (out of DP-matrix) and fixed plot for different recursion levels

  smarco

  committed
  9482ba5

Commits on Mar 7, 2023

• Refactor wf_init functions

  smarco

  committed
  b3755f6

Commits on Feb 24, 2023

• Updated CIGAR module (SAM-compliant CIGARs and simple mem-alloc)

  smarco

  committed
  2f70b65

Commits on Feb 20, 2023

• Manual merge with MAIN (to include CMakeFiles and other build features from Pjotr Prins (@pjotrp)

  smarco

  committed
  5557074

• Fixed bug on biwfa-lambda

  smarco

  committed
  edfc6ef

• Introduced wavefront_sequences_t object

  smarco

  committed
  041a7f2

Commits on Sep 2, 2022

• Merge branch 'development' of github.com:smarco/development into development

  smarco

  committed
  8569d47

Commits on Aug 27, 2022

• update tools and examples

  AndreaGuarracino

  committed
  fe1e1d6

Commits on Aug 9, 2022

• Added interface (C/C++) to wfmash heuristics and align-benchmark option --wfa-max-score

  smarco

  committed
  e0a647c

Commits on Aug 1, 2022

• Small code updates: refactor, checks, plot

  smarco

  committed
  98b16f7

Commits on Jul 30, 2022

• Improved plotting

  smarco

  committed
  8f0ee5d

Commits on Jul 25, 2022

• Refactored componen-begin/end and align-benchmark

  smarco

  committed
  070b884

• Refactor: CIGAR as a pointer object

  smarco

  committed
  0a2f047

• Refactor bialign->aligners

  smarco

  committed
  d641526

• Refactored to unialign module and debug

  smarco

  committed
  062bd8f

Commits on Jul 24, 2022

• Refactor and added Utests

  Show description for 6e45427
  smarco

  committed
  6e45427

Commits on Jul 11, 2022

• Fixed bug on BiWFA fallback

  smarco

  committed
  7659ccb

Commits on Jul 10, 2022

• Fixed bug on biwfa (sometimes it outputed (+/-G_o) score, CIGARS were correct)

  smarco

  committed
  6d43da2

• Implemented BiWFA+Heuristics+CutOffs and patched cases when heuristics make impossible find the alignment (WFA and BiWFA)

  smarco

  committed
  adba5b0

Commits on Jul 6, 2022

• - Implemented Eizenga's M!=0 formula to allow any match score

  Show description for bdb09fa
  smarco

  committed
  bdb09fa

Commits on Jun 10, 2022

• Added debug info for biwfa

  smarco

  committed
  3506562

Commits on Apr 23, 2022

• Updated generate-datasets, align-bench menu, and utests

  smarco

  committed
  14122ca

Commits on Apr 21, 2022

• Integrated BiWFA-gapAffine as ultralow memory mode (for the moment)

  smarco

  committed
  7f3e842

• Making room for BiWFA (support functions)

  smarco

  committed
  3ba8a98

Commits on Apr 4, 2022

• Improved Slab module to use less memory and be more lighweight

  smarco

  committed
  418777c

Commits on Apr 2, 2022

• Intra-parallel implementation (computeNext & Extend)

  smarco

  committed
  8048cb6

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