Code

biWFA it#288

Code

Merged

ekg merged 32 commits intomainwaveygang/wfmash:mainfrom biwfa-itwaveygang/wfmash:biwfa-itCopy head branch name to clipboardOct 30, 2024

+308-165

Commits

Commits on Oct 25, 2024

• Here is the one-line commit message for the changes:

  Show description for 95c8014
  ekg

  committed
  95c8014

  Copy full SHA for 95c8014

• feat: Add biWFA alignment logic to wflign.cpp

  ekg

  committed
  3ffcab8

  Copy full SHA for 3ffcab8

• fix: Move wfa_convex_penalties declaration earlier

  ekg

  committed
  d576563

  Copy full SHA for d576563

• fix: Move wfa_convex_penalties definition earlier

  ekg

  committed
  b9c2727

  Copy full SHA for b9c2727

• fix: move wfa_convex_penalties definition before first use

  ekg

  committed
  ba3f458

  Copy full SHA for ba3f458

• fix: Set penalties for wfa convex in wflign.cpp

  ekg

  committed
  00b27a1

  Copy full SHA for 00b27a1

Commits on Oct 27, 2024

• fix: Remove duplicate declaration of wfa_convex_penalties

  ekg

  committed
  3307042

  Copy full SHA for 3307042

• fix: move declaration of wfa_convex_penalties before first use

  ekg

  committed
  ec4b7b9

  Copy full SHA for ec4b7b9

Commits on Oct 28, 2024

• okify the declaration of convex penalties

  ekg

  committed
  1bafd4e

  Copy full SHA for 1bafd4e

• fix: Add missing do_biwfa_alignment() function implementation

  ekg

  committed
  1ba06a3

  Copy full SHA for 1ba06a3

• fix: Replace write_sam_alignment with write_merged_alignment

  ekg

  committed
  4278901

  Copy full SHA for 4278901

• fix: feat: Replace write_sam_alignment with write_merged_alignment and adapt parameters

  ekg

  committed
  ed9b5ab

  Copy full SHA for ed9b5ab

• fix: reverse logic to make biWFA the default aligner

  ekg

  committed
  c11e239

  Copy full SHA for c11e239

• feat: Add option to force WFLign alignment

  ekg

  committed
  69a2631

  Copy full SHA for 69a2631

• feat: Add force_wflign variable to WFlign class

  ekg

  committed
  9602bfd

  Copy full SHA for 9602bfd

• feat: Add force_wflign parameter to align::Parameters struct

  ekg

  committed
  beedda8

  Copy full SHA for beedda8

• fix: fix incorrect logic for choosing between WFlign and biWFA

  ekg

  committed
  78154a3

  Copy full SHA for 78154a3

• fix: Correct the logic for force_wflign in wflign.cpp

  ekg

  committed
  da5aa07

  Copy full SHA for da5aa07

• line

  ekg

  committed
  75d52f8

  Copy full SHA for 75d52f8

• match asm20/defaults for mm2 in biwfa params

  ekg

  committed
  bf6f63b

  Copy full SHA for bf6f63b

• fix: Set default chain gap to 2k

  ekg

  committed
  92660ca

  Copy full SHA for 92660ca

• feat: update help text for chain-gap default value

  ekg

  committed
  a14e4b4

  Copy full SHA for a14e4b4

• fix: Properly manage alignment_t objects in wflign

  ekg

  committed
  f8d9fa9

  Copy full SHA for f8d9fa9

• fix: Dereference alignment_t pointer before passing to write_alignment_paf

  ekg

  committed
  907a16e

  Copy full SHA for 907a16e

• fix: Use biWFA for smaller sequences or very high identity matches

  ekg

  committed
  263321c

  Copy full SHA for 263321c

Commits on Oct 29, 2024

• fix: Remove redundant alignment cleanup

  ekg

  committed
  62e6e9f

  Copy full SHA for 62e6e9f

• fix: Prevent double-free of alignments in write_merged_alignment()

  ekg

  committed
  e1884c0

  Copy full SHA for e1884c0

Commits on Oct 30, 2024

• refactor: Use biWFA alignment directly instead of WFline

  ekg

  committed
  9017734

  Copy full SHA for 9017734

• feat: declare do_biwfa_alignment function in wflign.hpp

  ekg

  committed
  f4a106e

  Copy full SHA for f4a106e

• fix: Comment out pt:Z:true and iv:Z:false tags in SAM and PAF output

  ekg

  committed
  eb3b735

  Copy full SHA for eb3b735

• fix: Add missing semicolon in write_alignment_sam function

  ekg

  committed
  e63c51f

  Copy full SHA for e63c51f

• remove dup of biwfa alignment function

  ekg

  committed
  2fbdef1

  Copy full SHA for 2fbdef1