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
Added more wrappers for functions that make system calls

Added the following wrappers that check the results of system calls
and exit non-zero if something went wrong.  This is so bwa can be more
robust against system failures (e.g. IO errors from remote storage, or
running out of memory).  The existing and new wrappers have also been
modified so that they no longer try to dump core on failure.  In most cases
the resulting core files are not useful (especially if bwa was compiled
with optimization turned on) so just pollute whatever directories they
got written to.

Wrappers for memory allocation functions:

xcalloc
xmalloc
xrealloc
xstrdup

New wrappers for IO functions:

err_fread_noeof   (also dies on EOF)
err_gzread
err_fseek
err_rewind
err_ftell
Use wrapper functions to catch system errors

Use the wrapper functions in utils.c plus a few extra bits of error
checking code to catch system errors and exit non-zero when they occur.