Martinsos/opal

Issues

• Segmentation fault for certain gap open / gap extension configuration

  #33 opened a year ago by michal-kierzynka
  0

• no member named 'abs' in namespace 'std';

  #30 opened 8 years ago by FadelBerakdar
  1

• Improve alignment speed

  #17 opened 10 years ago by Martinsos
  3

• Add E-value

  #31 opened 8 years ago by Martinsos
  0

• Add SHW mode

  #29 opened 9 years ago by Martinsos
  0

• When gap open is smaller then gap extend, stuff breaks

  #28 opened 9 years ago by Martinsos
  0

• Add flag for turning off overflow check

  #27 opened 9 years ago by Martinsos
  0

• Slowdown after new feature

  #11 opened 9 years ago by Martinsos
  2

• Add flag to choose if end location is needed (to make search faster)

  #14 opened 9 years ago by Martinsos
  1

• report GCUPS for opal_aligner ?

  #26 opened 9 years ago by jeffdaily
  3

• Process multiple cells in one iteration, add padding to database sequences, optimize for cache

  #3 opened 10 years ago by Martinsos
  3

• Alignment of data for SSE/AVX does not seem to matter

  #25 opened 10 years ago by Martinsos
  0

• deleted

  #24 opened 10 years ago by Martinsos
  0

• Improve speed of basic search

  #23 opened 10 years ago by Martinsos
  4

• Automatize comparison with other aligners and performance tests

  #22 opened 10 years ago by Martinsos
  0

• Create example of usage

  #21 opened 10 years ago by Martinsos
  0

• Update README!

  #20 opened 10 years ago by Martinsos
  0

• Make function input more flexible

  #15 opened 10 years ago by Martinsos
  1

• Split swimd.cpp into more files

  #19 opened 10 years ago by Martinsos
  0

• Limit memory usage of alignment

  #18 opened 10 years ago by Martinsos
  0

• Implement calculation of alignment

  #1 opened 10 years ago by Martinsos
  6

• Consider using swimd to solve 1:1 for large targets

  #16 opened 10 years ago by Martinsos
  0

• Implement finding location in target and query where best score was found

  #13 opened 10 years ago by Martinsos
  1

• Difference between swimd and edlib

  #12 opened 10 years ago by rob-p
  2

• scores are often incorrect

  #10 opened 10 years ago by tolot27
  11

• calculate hits for all query sequences of a multiple fasta file

  #9 opened 10 years ago by tolot27
  1

• make command line parameters compatible to blast/swipe

  #6 opened 10 years ago by tolot27
  2

• Add callback function that is called after sequence is calculated

  #5 opened 10 years ago by Martinsos
  0

• Write better tests

  #4 opened 10 years ago by Martinsos
  0

• Implement AVX2 version

  #2 opened 10 years ago by Martinsos
  1