Merge pull request #1 from ppliu/master

added paired end functionality for STAR.scala
updated STAR script and added normalize bedgraph
added oldsplice wrappers
updated splicing scripts
added RNASeqQC runners
fixed bugs in splicing and rnaseqc code
updated custom runners to be path free
fixed many issues with internal yeo-scripts
added editing and miso to pipeline
added new clip-seq peak calling methods
updated genome coverage to deal with both single and double stranded data
updated STAR to not have typo when reporting additional bam features
added job limit argunment
updated gene locations on tscc
added proper timing for rna-editing and corrected name for piranah
added more stringent output filtering for mapping
Merge branch 'master' of github.com:gpratt/gatk

* 'master' of github.com:gpratt/gatk:
  added proper timing for rna-editing and corrected name for piranah
  updated gene locations on tscc
  added job limit argunment
  updated STAR to not have typo when reporting additional bam features
  updated genome coverage to deal with both single and double stranded data
  added new clip-seq peak calling methods
  added editing and miso to pipeline
  fixed many issues with internal yeo-scripts
  updated custom runners to be path free
  fixed bugs in splicing and rnaseqc code
  added RNASeqQC runners
  updated splicing scripts
  added oldsplice wrappers
MISO always in single end mode because insert lengths can be crazy and we want to use every read we can get
added more stringent output filtering for mapping
MISO always in single end mode because insert lengths can be crazy and we want to use every read we can get