Difference: NGSAlignerDiscussion (2 vs. 3)

• The main core of any tool is a Driver
• A typical driver requires:
  • FastqFile to read input
  • SamFile to write output
  • Mapper for mapping reads to the reference
    • Contains an Index holding the reference
      • The Index requires the refernece from a FastaFile (not shown)
    • May optionally use an Aligner
  • MatchMaker for post-processing pair-end reads, if applicable
    • Requires access to an Index and an Aligner

• The typical way to build an aligner executable is as follows:
  1. FastaFile to read refernece
  2. create an Index by loading or building a new one
  3. create an Aligner with user-set penalty values
  4. create a Mapper using the above two objects
  5. create a MatchMaker only if dealing with pair end (PE) reads
  6. create a FastqFile (or two in PE), using files with reads
  7. create a SamFile
  8. create a Driver using the above three (or four, for PE)
  9. Run() the Driver

I don't see anything horribly wrong with it... as it's built various usable aligners, but I don't see anything wonderful about it either, being built without much planning.

-- Main.jujubix - 26 May 2010