Don't use fully-qualified paths in javadoc.
Add `SamReaderFactory` as a new facility for reading from SAM files.
- Produces `SamReader` objects, which are similar to `SAMFileReader`.
- Deprecate `SAMFileReader`, as `SamReaderFactory` is the preferred approach to creating things that read SAMs.  `SAMFileReader` still functions as normal.
- See `SamReaderFactory`'s javadoc for examples of how to use it.
Merge pull request #1 from samtools/mm_sam_reader_factory_and_friends_and_their_cousins

Add `SamReaderFactory` as a new facility for reading from SAM files.
Make sure BAM index file is newer than BAM file
Merge pull request #7 from samtools/jg_pfb409

Make sure BAM index file is newer than BAM file
Add more backwards compatability for loading metrics in "legacy" packages.
Merge pull request #8 from samtools/mm_bugfix_legacy_metrics

Add more backwards compatability for loading metrics in "legacy" packages.
initial cram code base commit
changed Log dependency from net.sf to htsjdk.samtools;
renamed SAMIterator to make it obvious this is CRAM related.
Merge branch 'cram_code_base' of https://github.com/samtools/htsjdk.git into cram_code_base
added CRAM file type to SamReader and refactored CRAMFileReader
according to new SamReader paradigm