Merge pull request #255 from andrewjpage/pipeline

update schema to 26
RNASeqExpression using 2 processors
Merge pull request #256 from carlacummins/updated-rna

RNASeqExpression using 2 processors
filter out perfect pairs before improvement
define self
dont set full directory for bam 2 fastq
Merge pull request #257 from andrewjpage/map_reads_before_improvement

Map reads before improvement
Updated RNASeqExpression.pm bsub options
Merge pull request #258 from carlacummins/updated-rna

Updated RNASeqExpression.pm bsub options
Unmapped bam file produced by tophat is now merged properly into the accepted hits bam file
Finished test suite for the new accepted hits and unmapped functionality in the tophat wrapper module
Merge pull request #259 from js21/pipeline

Unmapped reads are now merged by default when mapping with tophat