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Removed BWA Functionality

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Toni Westbrook edited this page May 24, 2015 · 2 revisions

The following functionality has been removed from the BWA source as it is not applicable to/required by PALADIN at this time, or may be low priority. Applicable functionality may be modified and added back in the future (refer to this list):

  • PAC2BWTGEN (bwt_gen., QSufSort.) - This contains code by Wong Chi Kwong that is an alternative implementation of the BWT generation routines. From forum posts, I gathered this was implemented as the default version of the PAC2BWT code (which is used in PALADIN) breaks on references larger than 2GB. References of this size not a priority for now.
  • ALN algorithm (bwtaln., bwtgap., bwase., bwape.) - Older ALN algorithm - we've focused implementation on the MEM algorithm
  • BWTSW2 algorithm (bwtsw2*) - Older BWTSW2 algorithm - we've focused implementation on the MEM algorithm
  • Lite implementations (lite) - only focusing on full MEM algorithm
  • Misc supporting (example.c) - not applicable/needed

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