move mem_fill_scmat() to bwa.{h,c}
bwa-sw: use bwa_gen_cigar() for cigar generation
bwa-sw: ditch stdaln
replace aln_global in bwase.c
r329: ditch stdaln.{c,h}; no changes to bwa-mem

stdaln.{c,h} was written ten years ago. Its local and SW extension code are
actually buggy (though that rarely happens and usually does not affect the
results too much). ksw.{c,h} is more concise, potentially faster, less buggy,
and richer in features.
Fixing problem with linking to libm on some Ubuntu systems (I see this on machine running 11.04, kernel 3.0.0-14-virtual).  Changing order of -lm on the command line seems to do the trick and should be tolerated in other environments.
Merge pull request #14 from drkeoni/master

Small fix for possible compile problem on Ubuntu systems
r331: rewrote CIGAR generation for bwa-short

When backtracking, bwa-short does not keep the detailed alignment or the exact
start and end positions. To find the boundary and the CIGAR, the old code does
a global alignment with a small end-gap penalty. It then deals with a lot of
special cases to derive the right position and CIGAR, which are actually not
always right. It is a mess.

As the new ksw.{c,h} does not support a different end-gap penalty, the old
strategy does not work. But we get something better. The new code finds the
boundaries with ksw_extend(). It is cleaner and gives more accurate CIGAR in
most cases.
r332: added output threshold

Otherwise there are far too many short hits
De-overlap paired-end reads
r334: added pemerge to bwa
r335: fixed a compiling error

Caused by the last change
r336: fine tuning pemerge
r337: mem - always read even number of reads

In the old code, we may read odd number of reads from an interleaved fastq.
r338: pemerge - fixed memory leaks; multithreading

pemerge is actually quite slow.
r339: pemerge - expose some settings to CLI
r340: feature freeze; updated the manpage

I will stop adding new features to bwa and prepare for the next release. I will
briefly evaluate the variant calling accuracy before the release.
r341: bugfix - wrong mate position

when one end is mapped with a score less than -T. Caused by the -T option.
Merge branch 'master' into master_fixes

Conflicts:
	Makefile
	bwape.c
	bwase.c
	bwtsw2_aux.c
	stdaln.c