Genomedata

* Removed platform specific builds from distribution

* fixed bug related to updated PyTables
* compile works with HDF5 setups even when they were built
--with-default-api-version=v16
* doc fixes
* fixed DeprecationWarnings associated with PyTables 3.0
* updated dependency to PyTables >= 3.0

* genomedata-query: new command that prints data from a Genomedata archive for your
non-Python scripting needs (thanks to Max Libbrecht)
* genomedata-histogram: new command that prints histograms from a Genomedata archive
(combination of a new module by Max Libbrecht and an old module by Michael Hoffman)
* genomedata-info: add "contigs" subcommand (thanks to Max Libbrecht)
* genomedata-info: friendlier error when unsupported command name used
* genomedata-load-data: friendlier errors when invalid BED3+1/bedGraph data supplied
* genomedata-load-seq: always makes chromosome and supercontig
coordinates with unsigned 32-bit integers instead of system int
* genomedata-load-data: more detailed error message when initial file open fails
* genomedata-load-data: bugfix
* now compile with -Wextra
* doc fixes

* API: now allow array of tracks. For example: chromosome[245:270, array([7, 5])]

* API: now allow lists of tracks when directly accessing chromosome data, for example:
chromosome[245:270, ["data1", "data3"]] or chromosome[245:270, [7, 5]]
* genomedata-load-seq: add --assembly option which supports AGP files,
to allow avoid loading seq while still dealing with assembly gaps
properly
* genomedata-load: now supports --assembly and --sizes options
* genomedata-load-assembly: alias for genomedata-load-seq.
genomedata-load-seq will be deprecated in the future
* genomedata-load-data: now support DOS-style line endings ("\r\n")
* genomedata-load: print genomedata-load-data error code on failure
* genomedata-load-data: print more informative messages when ignoring data
* genomedata-load: all diagnostics messages to stderr
* genomedata-load: some diagnostics now include timestamp so we can
see where performance bottlenecks are
* genomedata-load: more descriptive error messages
* genomedata-load-seq: print more descriptive error message when
attempting to load sequence from a non-FASTA file
* genomedata-load: fixed issue 10: now compiles on gcc 4.6.2
* docs: add links to source code
* docs: genomedata-load: sequence "option" is mandatory. In a future
version, we should change this to an argument to reflect this.
* test: add tests for DOS-style line-endings

* genomedata supercontigs are no longer guaranteed to have seq data
* add --sizes option to genomedata-load-seq, to allow avoid loading seq
* Genome.add_track_continuous() has a significant performance
improvement. This also means that genomedata-open-data will run much
faster, as well as genomedata-load-data on fresh tracks
* fix bug where genomedata-load-seq didn't work
* fix bug where directory genomedata archive didn't work with only one chromosome