On 18/07/11 13:04, David Eccles (gringer) wrote:
> It's also slower than sebhtml/ray (Total: 25 seconds vs 14 seconds; 57
> seconds if I include asserts and debug symbols). I presume this is
> because of the additional complexity for getOutgoingEdges / getLastCode
> (it needs to re-calculate the last base each time by iterating through
> the k-mer). Perhaps the k-mer should store the last base as well as the
> first....

So, I implemented a different k-mer format that included a last-base 
(reducing the max k-mer size for the same number of bytes by 1), and 
have worked out that this speed difference isn't only because of the 
re-calculation:

--- With colour-space matching ---
  Sequence partitioning: 1 seconds
  K-mer counting: 4 seconds
  Coverage distribution analysis: 0 seconds
  Graph construction: 8 seconds
  Edge purge: 0 seconds
  Selection of optimal read markers: 6 seconds
  Detection of assembly seeds: 0 seconds
  Estimation of outer distances for paired reads: 1 seconds
  Bidirectional extension of seeds: 0 seconds
  Merging of redundant contigs: 1 seconds
  Generation of contigs: 0 seconds
  Scaffolding of contigs: 0 seconds
  Total: 21 seconds

--- With base-space matching ---

  Sequence partitioning: 0 seconds
  K-mer counting: 3 seconds
  Coverage distribution analysis: 0 seconds
  Graph construction: 5 seconds
  Edge purge: 0 seconds
  Selection of optimal read markers: 3 seconds
  Detection of assembly seeds: 1 seconds
  Estimation of outer distances for paired reads: 0 seconds
  Bidirectional extension of seeds: 1 seconds
  Merging of redundant contigs: 0 seconds
  Generation of contigs: 0 seconds
  Scaffolding of contigs: 0 seconds
  Total: 13 seconds

-- David

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