Somaticseq

* 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.

* Updated some docker job scripts.
* Added a script that converts some items in the VCF's INFO field into the sample field, to precipitate the need to merge multiple VCF files into a single multi-sample VCF, i.e., utilities/reformat_VCF2SEQC2.py.
* No change to somaticseq algorithm.

* Restructured the utilities scripts.
* Added the utilities/filter_SomaticSeq_VCF.py script that "demotes" PASS calls to LowQual calls based on a set of tunable hard filters.
* BamSurgeon scripts invokes modified BamSurgeon script that splits a (proper) BAM file without the need to sort by read name.
* No change to SomaticSeq algorithm

* Added run script generators for dockerized BAMSurgeon pipelines at utilities/dockered_pipelines/bamSurgeon
* Added an error message to r_scripts/ada_model_builder_ntChange.R when TrueVariants_or_False don't have both 0's and 1's.
* No change to SomaticSeq algorithm.

* Improved pipeline script generator, but still consider them experimental.
* No change to SomaticSeq algorithm