I'm trying to work through this big Kmer colour-space change, and I'm getting a little stuck because there's Kmer manipulation code all over the place. While I was running through the unit tests to try to weed out code that touches Kmers (to be shifted into the Kmer class), I came across the _getOutgoingEdges / _getIngoingEdges functions, and can't work out what they are trying to do.
The comments for these functions don't really mention anything about the purpose of the function, which makes it difficult for me to work out how to implement it for the modified Kmer structure: [_getOutgoingEdges] /* * abcd efgh * 00ab 00ef * 00ab cdef */ [_getIngoingEdges] // 1 0 // // 127..64 63...0 // // 00abcdefgh ijklmnopqr // initial state // abcdefgh00 klmnopqr00 // shift left // abcdefghij klmnopqr00 // copy the last to the first // 00cdefghij klmnopqr00 // reset the 2 last I get that it's moving sequence around, and that 'ab' describes a 2-bit location, rather than 2 base-pairs, but that's about the limit of my guesses. There's a mention of 'changing the hash value of the Kmer', which I presume happens when you have un-used bits in the Kmer (e.g. with kmer length 20). Can anyone offer any other insights to this? Oh, and BTW, there may be range check problems in the current code (1.6.0+) with Kmer sizes greater than 100. The kmerAtPosition function uses char sequence[100] together with memcpy, then overwrites sequence[wordSize] with a null character (even if wordSize > 100). I'm not sure what the effect of this is, but it probably shouldn't be doing that. -- David ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
