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
Merge branch 'master' into api
r124: updated version number
rename the "api" branch as "master"
r126: release bwa-0.6.2
Do not inline functions used externally

Compiling using CLANG gives the following errors:
Undefined symbols for architecture x86_64:
  "_bwt_occ", referenced from:
      _bwt_cal_sa in bwt.o
      _bwt_sa in bwt.o
  "_bwt_2occ", referenced from:
      _bwt_match_exact in bwt.o
      _bwt_match_exact_alt in bwt.o
      _bwt_cal_width in bwtaln.o
  "_bwt_2occ4", referenced from:
      _bwt_match_gap in bwtgap.o
      _bsw2_core in bwtsw2_core.o
  "_bwtl_2occ4", referenced from:
      _bsw2_core in bwtsw2_core.o
Merge pull request #11 from sjackman/inline

Do not inline functions used externally
resolve duphits after right extension as well
r128: more conservative chaining filter
Merge branch 'master' of github.com:lh3/bwa
r131: r128 plus remote changes
r132: optionally copy FASTA/Q comment to SAM
preparation for further changes
fixed a couple of unimportant bugs in SMEM