Somaticseq

* Added another feature: consistent/inconsistent calls for paired reads if the position is covered by both forward and reverse reads. However, they're excluded as training features in SomaticSeq.Wrapper.sh script for the time being.
* Change non-GCTA characters to N in VarDict.vcf file to make it conform to VCF file specifications.

* Optimized memory for singularity scripts
* Updated bamQC.py and added trimSoftClippedReads.py in utilities
* Added some dockered scripts at utilities/dockered_pipelines/QC
* No change to core SomaticSeq algorithm

* Incorporated TNscope's output VCF into SomaticSeq, although it's not a part of the dockerized somatic mutation workflow.

For paired tumor-normal workflow and bam simulation workflow, singularity-compatible scripts are located at utilities/singularities, with the same commands as dockerized workflows at utilities/dockered_pipelines.

* Additional passable parameters options to pass extra parameters to somatic mutation callers. Fixed a bug where the "two-pass" parameter is not passed onto Scalpel in multiThreads scripts (although I have extensively tested --two-pass parameter and found it to have ZERO effect).
* Ignore Strelka_QSS and Strelka_TQSS for indel training in the SomaticSeq.Wrapper.sh script.

* Fixed the bug where "CD4" in the output VCF file where alternate concordant reads where grabbed twice, when it should've been alternate concordant and then alternate discordant read.
* Added (limited) tumor-only support.
* Convert VarDict's "Complex" variants into SNVs when appropriate.
* Slightly modified r_scripts/ada_model_builder_ntChange.R script, i.e., the arguments succeeding the input TSV file are features to be ignored in training.