htsjdk version 1.124

htsjdk version 1.124
Fixing Java 8 compilation issues with type casting
htsjdk version 1.125

htsjdk version 1.125
htsjdk version 1.126

htsjdk version 1.126
Always flush outputStream, regardless of instanceof FileOutputStream
Merge pull request #137 from mbreese/master

Always flush outputStream, regardless of instanceof FileOutputStream
Fixed broken unit test (remote file had been moved to a new location).  Updated the location of the remote file to one under picard group control.
Merge pull request #138 from samtools/gg_fixBrokenTabixReaderTest

Fixed broken unit test (remote file had been moved to a new location).
Make SortingVariantContextWriter public.
Currently, the only way to access this functionality is through VariantContextWriterFactory.sortOnTheFly,
but VariantContextWriterFactory is deprecated.
Master rebase and fixups for deprecations.
initial cram code base commit
added lossy options to CRAMFileWriter;
force lossless mode by default if no policies are given
lazy init of qs preservation with "*8"
Updated htsjdk to use SamReader instead of the deprecated SAMFileReader.
Also fixed a bug in the tlen calculation for cram compression records.
Added setOption and reapplyOptions methods to SamReaderFactory.
Deprecated truncated reader.
Exposed file extension from Type.
Added reference fasta to SamReaderFactory and SamWriterFactory to facilitate CRAM support.
Use SamReaderFactory makeDefault with reference sequence whenever possible to allow for CRAM support.
fixed the multiref slice building code.
relaxed EOF marker by ignoring ITF8 hanging bits
initial commit of indexing for CRAM
added static methods for CRAI parsing and building in-memory index
added crai building methods that takes input stream
fix for pairing primary and secondary alignments separately when writing
Merge pull request #140 from samtools/jc_cram_changes

Jc cram changes
Merge pull request #133 from iliat/google-fixes

Fixing Java 8 compilation issues with type casting
50% faster nybble to byte conversion by using a lookup table instead of a switch statement
Merge pull request #130 from BeatWolf/FastByteDecompression

Speedup SAMUtils.compressedBasesToBytes for faster BAM file parsing
Update build.xml

Update htsjdk to 1.127
Merge pull request #141 from samtools/aw_sorting_vcf_writer_public

Make SortingVariantContextWriter public.
VCFFileReader:
Added functionality so that fromVCF can create an intervalList with or without filtered variants (defaulting to without, as currently)
Added functionality to fromVCF so that the intervals will end at the END value from the info field (if available).