r132: optionally copy FASTA/Q comment to SAM
preparation for further changes
fixed a couple of unimportant bugs in SMEM
bugfix: min_intv not working in SMEM
a bit refactoring for further changes
move smem iterators to bwamem.{c,h}
code backup
basic chaining working

Definitely suboptimal in a lot of corner cases...
bugfix: wrong B-tree comparison
no effective changes
typo in comments
reseed long SMEMs
code cleanup; added a missing file
bugfix: memory leak
routine to get subsequence from 2-bit pac
code backup
reimplemented SW extension; not tested yet
code backup; it is wrong
bugfix: the first line is wrong
no effective changes