initial commit for 2.0;
changed version and build number;
added preliminary cram2 files for testing.
'small.cram' reading test is ok.
fixed '*' QS in Sam2BamRecordFactory.addInsertions.
2.0 prototype in progress, smallcram tests ok but LTF8 tests fail.
roundtrip in TestContainer passes ok.
added SM and SC; working on index
bam2cram+cram2bam work on the small.bam file.
fixed bit flags reversed order and subs matrix.
fixed AP to slice context.
fixed bit flags to pad 0x8 and 0x20, these are always 0.
removed UNKNOWN read group, -1 is used for no read group index;
NS -1 is used for no mate.