light cleanup
bam-rmdup can now handle multimapped reads

The way it's done is by dropping all the additional alignments, then
treating the rest as if only one alignment was ever reported.  The
default is still to bail out as soon as NH>1, IH>1 or HI>1 are
encountered.
fix removeExt
cleanup
bump version number
rudimentary SAM writing

This is mostly intended for debugging... if you print SAM for
processing, you need professional help.
actual SAM output
Merge branch 'master' into genotyper
compilable 'decompose' function

Function that breaks a read into pieces useful for genotype calling.
Don't expect it to work just yet.