V2.0.0 release

• run regression tests (+backup on colosse)
• run unit tests 2012-06-20
• check version in Makefile 2012-06-20
• ./Ray -help > MANUAL_PAGE.txt 2012-06-20
• compile with make 2012-06-20
• compile with cmake 2012-06-20
• git tag vx.y.z
• git checkout tag,
• do a tar.bz2, compile it (make + make install) and test it
• upload the tarball on sf
• update the web site (download + manual)
• post an email on the list including changes (dump-changes)
• update the seqanswer thread

Ray 7102b16f1f282a0003f9982b42a3a744d9bffe59

validation with MUMMER:

misassembledContigs contains small indels too, which are not really a problem at that scale.

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 coli.Ray & 66 & 60 & 4593129 & 69592 & 134245 &  222309 &  0.9924 & 5 & 0 & 36 & 6 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 coli-interleaved.Ray & 68 & 61 & 4599008 & 67632 & 134245 &  222309 &  0.9934 & 4 & 0 & 36 & 6 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 ecoli-MiSeq.Ray & 92 & 83 & 4584978 & 49836 & 95817 &  268554 &  0.9850 & 2 & 0 & 33 & 25 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 L1-L3.Ray & 8 & 4 & 4646253 & 580781 & 1090091 &  1509013 &  0.9857 & 5 & 0 & 69 & 47 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 multiple-peaks.Ray & 2 & 1 & 873283 & 436641 & 815918 &  815918 &  0.9999 & 2 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pg2.Ray & 6 & 6 & 874820 & 145803 & 614763 &  614763 &  0.9984 & 0 & 0 & 1 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 phix.Ray & 1 & 1 & 5386 & 5386 & 5386 &  5386 &  1.0000 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-interleaved-bz2.Ray & 77 & 56 & 6226244 & 80860 & 183096 &  572252 &  0.9962 & 2 & 1 & 1 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-p.Ray & 1666 & 1666 & 6051984 & 3632 & 5894 &  48599 &  0.9659 & 1 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-p-bz2-gz.Ray & 1661 & 1661 & 6053235 & 3644 & 5917 &  48599 &  0.9661 & 2 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-s.Ray & 1675 & 1675 & 6053567 & 3614 & 5872 &  48599 &  0.9662 & 1 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept.Ray & 0 & 0 &  &  &  &   &  0.0000 &  &  &  &  \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-200.Ray & 95 & 92 & 2004757 & 21102 & 39231 &  128046 &  0.9860 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-300.Ray & 78 & 69 & 2017890 & 25870 & 48703 &  183041 &  0.9945 & 0 & 0 & 1 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-amos.Ray & 95 & 92 & 2004109 & 21095 & 39231 &  128046 &  0.9854 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-bz2.Ray & 95 & 92 & 2004109 & 21095 & 39231 &  128046 &  0.9854 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-interleaved.Ray & 95 & 92 & 2004109 & 21095 & 39231 &  128046 &  0.9854 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-interleaved-bz2.Ray & 95 & 92 & 2004328 & 21098 & 39231 &  128046 &  0.9855 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-simulated-errors.Ray & 96 & 81 & 2005869 & 20894 & 37594 &  127941 &  0.9884 & 0 & 0 & 0 & 0 \\