reads only split into 2 parts and 4 parts to aln
add lkt
rename the Rpart index name
separated sam related func from aln and be a independent module
fix the bug in sam.c
1.seq will be read once to finish 0-3mismatch
branch alnpe, but still can't work
fix some bugs, but still can't work
fix some bugs, still can't work
fix some bugs, can't work
fix some bugs, can't work
fix some bugs;can be compiled;bug can't work
rm bwtsw
fix a bug in macro PRINT_TIME(in alnse.c)
fix some bugs
rm some files
fix some bugs
fix some bugs
fix some bugs
small changes