[Denovoassembler-devel] Why flush both k-mer and its complement?

[David E. (gringer) <dav...@mp...>]

I notice that in assembler/KmerAcademyBuilder.cpp:120-139 you have:

120 rankToFlush=m_parameters->_vertexRank(&a);
121 [add <rankToFlush> to pending flush messages]
130 Kmer b = 
complementVertex(&a,wordSize,m_parameters->getColorSpaceMode());
132 rankToFlush=m_parameters->_vertexRank(&b);
133 [add <rankToFlush> to pending flush messages]

but the vertexRank function returns the hash of the lowest k-mer:

core/Parameters.cpp:1200 (_vertexRank)
return vertexRank(a,m_size,m_wordSize,m_colorSpaceMode);

core/common_functions.cpp (vertexRank)
134 Kmer b=complementVertex(a,w,color);
135 if(a->isLower(&b))
136     b=*a;
137 return hash_function_1(&b)%(_size);

So the code appears to be doing 3 complement vertex operations 
(KmerAcademyBuilder.cpp:130, common_functions.cpp:134 * 2) for each 
flush. Could the second flush (i.e. KmerAcademyBuilder.cpp:130-139) be 
removed without loss of function?

-- David