New parameter defaults for NGS copy number segmentation tool.
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Increase session replay test timeout to three hours
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.
Making Microarrays/Utilities/Extract samples from dataset less sensitive about phenodata column names.

When reading in the phenodata, by default R will check that column names are valid R variable names (e.g. cannot contain spaces or start with a number). As the user interface allows users to create illegal column names in phenodata (like containing spaces), this can break tools that have a METACOLUMN_SEL parameter, as the column names in the phenodata read into R will no longer be the same as was displayed in the user interface. This can be fixed by adding check.names=FALSE to the R command reading in the phenodata (of each and every tool), or alternatively by preventing creation of illegal column names in the phenodata in the user interface.
Merge remote-tracking branch 'upstream/master'
Replace whitespace characters in phenodata columns
Merge branch 'master' of https://github.com/chipster/chipster.git
Merge remote-tracking branch 'upstream/master'
Deal with missing parameters in SessionReplayTest
Bugfix for CNA / Count overlapping CNVs when parameter genome.build is set to the previous build NCBI36.