Added source code

• Added source code to public repo

Upgrade to pysam 0.8.1 or higher, specify pileups instead of bams

• Require pysam version 0.8.1 or higher to deal with API inconsistencies
• filterByReadSupport.py uses query_position instead of qpos to deal with pysam API inconsistencies
• Added ability to specify pileups as input instead of bams

Improve BLAT filter, require pysam 0.7.5

• Require pysam version 0.7.5 to stick with code using qpos
• Changed BLAT filter to use both the e-value and the identity scores. A read is valid if it has the highest of either of the scores.
• Changed mpileup filter to re-classify germline mutations without a high enough alternative allele percentage as possibly somatic.

Merge all chromosome files into one patient file, bug fixes

• Removed LOH code from radia.py
• Added script to merge all chroms
• Removed start and stop coordinates from header
• Fixed the summary numbers from radia mod types
• Fixed radia.py so that the version string will be printed when --version is specified
• Added the source prefix (e.g. "DNA_NORMAL") to the debug messages so you can see which file is being referenced
• Changed error message in radia.py that -a and -z cannot be equal, -z must be larger

First major release

• Added ability to include the number of filters that a variant overlaps with (e.g. number of self-chains)
• Added BLAT bug fix
• Added RNA editing filtering