uci-cbcl/genomix — pull request #60 by Nan-Zhang (2013-11-12 22:07:58+00:00)
Title: change the partial members of genomix-data, genomix-hyracks for adapting ray-style

@jakebiesinger @JavierJia @anbangx please give some feedback. I have changed some partial structure in genomix-data, and genomix-hyracks for adapting to ray-style. tests are not been completed but in works.
1. in ReadHeadInfo, add two VKmer field(mate0ReadSequence, mate1ReadSequence) to store the read sequence(initial plan is to use Kmer to store these stuff, but kmer_size was set to 55 initially, there may be some conflict if I use Kmer to store readSequence). The .equal(), .compare(), and .hashcode() have nothing to do with ReadSequence.
2. changed some functions in ReadHeadSet, Node, Graphviz for corresponding to the changes in ReadHeadInfo.
3. because we don't use the readIdSet in EdgeMap, So I use VKmerList to replace EdgeMap to store in Node.
4. changed hyracks-graphbuilding code for corresponding these above changes. Assume the inputFormat is: readId '\t'mate0Sequence'\t'mate1Sequence. (left sequence must come from mate0, right sequence must come from mate1)