bugfix: long-existing out-of-boundary bug
Tim's suggestion suffix file name with .64
do not use .64 suffix by default
check *.64.bwt first and then *.bwt
debugging code: bwasw has a rare bug
debugging; bug persistant
bugfix: incorrect bandwidth
updated revision number
commented out debugging code
API: aln seems working
towards refined gapped; unfinished
compute CIGAR; rev seq not working
preliminary doc
complete single-end alignment
simplified bwa_se() interface
updated APIs abit
unnecessary large .sai output
r115: added -I and -S to bwasw
Merge branch 'master' into api
r124: updated version number