add initial debian/
add samtools dependency
add gcc version requirement
remove useless Homepage line in control
correct packager email address
make dpkg-source ignore vendor/samtools*
add Makefile patch
put the executable in the deb
add zlib1g dependency
remove patch file
add patch queue
add debian/source/format to specify quilt usage
rewrite in c++
readability fixes
add -c option (chromosome) for parallel processing
better error checking for bam io
inline a few of the trivial BamEntry functions
refactor BamReader exception handling

readable
defer to RowAssigner for entry stop position

RowAssigner knows if it is needed or not, and it's kind of expensive to
calculate.
treat 0 returned from bam_iter_read as success