fix for ByteArrayLengthEncoding failing to parse params longer then
1024;
minor fix for unmapped reads sequence id.
fixed bugs in QSP; removed CramRecord boolean flags
removed boolean flags in CramRecord; added a temp test for Tim's bug of
no_ref != no_start.
quick fix for CramRecord flags.
rearranged and renamed classes related to cram format parsing and
writing.
working on cram io, in progress.
adding direct reader that writes BAM to memory, not tested.
testing new reader, fastq seems to work.
added ReferenceSource to combine ref look ups from file and internet;
introduced AbstractBitCodec to allow for optmizations.
further optimizations on reading, switched to IntHashMap and implemented
bulk read methods on codecs and readers;
added 'fastq' tool.
working on ReaderToBAM, works on small.cram
fixed issues with dataset 6178_5#1, seems ok but a deeper check may be
required.
wokring on ref tracks
fixed missing BaseQuality in ReaderToBAM, tests not complete.
fixed ref md5 issues
working on ena fixes and tools
ena fastq dump, not tested
fixed PG addition to the header;
added UI injection to SQ in the header.
WiP: fixes against scramble
2.0