fix: lower case ref bases carried over to reads;
fix: fails if first read is unmapped;
added: BAM index, preliminary, works;
pre-built jar
added View to view and merge BAM/CRAM files, not tested;
fixed BAM indexing, nearly complete, briefly tested.
BAM indexing tested;
renamed 'view' to 'merge' because 'bam' tools does most of the 'view'
functions.
fixed lossless QS alias, tested.
fixed null read bases bug.