Corrected typo in Bowtie2 tools.
Changes to Tophat2 tools.
Dimont tools commented out.
Trended dispersion removed.
Chromosomal coordinates added by default.
Made parametric fit default.
Manual updates.
Filtering default changed to 1.
Replace whitespace characters in phenodata columns
Merge branch 'master' of https://github.com/chipster/chipster.git
Deal with missing parameters in SessionReplayTest
Merge branch 'master' into data_beta