Merge pull request #6 from ICGC-TCGA-PanCancer/master

Merge pull request #5 from ICGC-TCGA-PanCancer/dev
Reworked to potentially support multiple tumours vs 1 normal.  Still needs cleanup code adding.
Forgot to set test true
Mapped wrong test file
Path error
Updated to attempt 10x simulated data analysis, set up as though a donor with 2 tumour samples.
possible issue in split character used in ini file, investigating
Docs suggest : and ; have special meaning, switched to ,
Add print to see what is happening
more debug
wasn't making bas array same size as tumour bam array.
Prevent log file clashes when multiple tumours for a single donor
Remove output redirection as it makes it difficult to debug
Remove some legacy params and switch test data.
Added installation details for algorithms
Resolves #7, ready for merge to dev, minor changes to vcfUpload may still be required.
Added missing paramter to ini, and made naming of variables relating to the control sample consistent  (rather than a mix if normal/control)
Make test/upload warnings more obvious during initialisation.
Copy paste error in script, also corrected some method accessibility in java.
Updated usage of vcfUpload section plus some extra params for testing purposes