Merge pull request #1 from stevenweaver/master

Indexing bam file in order for fetch to work
align: misc tweaks to aligner, small cleanups in scorematrices
bam2msa: only index when fetching a region
bam2msa: index in all cases, as that seems necessary
name score matrices, abstract some common parser options, msa2bam script, fix bug in calling compute_cigar from SamBamIO
add clipedge script for Sergei, increase flexibility of add_* parser options
make tabulating msas an order of magnitude faster
fix these spurious errors I encountered...