GenomeView 1514: short reads and coverage

In this release of GenomeView the visualization of individual short reads, as well as coverage plots has been significantly improved.

With directional RNA-seq the read sense is now visually indicated, even for paired-end data. Hovering over individual reads will show detailed information about each read. When reads of a pair overlap, this is visually indicated.

For coverage data, there is now support for the TDF file format. This format is a high-performance file format for coverage data. In the manual you can find instructions how to generate these files from an existing BAM file. This allows GenomeView to offer multiple aggregation functions (mean, min, max, median, percentiles, etc.) for coverage data at low resolution for little cost.

We have added some genomes to the Genome Explorer:
- Mycobacterium smegmatis
- Mouse (mm8 and mm9)

This release also fixes numerous bugs:
- pile up should only display matches when there is diversity data
- remove tick labels in feature filter, they are often wrong with double values
- pileup tasks properly return immediately when the model wants to exit
- fixed creating features with a new feature type
- changing the type of a feature properly works when typing a new type name
- when a data type is removed, it is properly unloaded from all chromosomes
- Improved stability on OS X
- don't draw SNP track if there is no data for the SNP track
- shortread track cannot be collapsed, so don't check on it
- added more default colors