Somaticseq

Fixed a minor bug where the number of indels within 3 bps of the variant site double-counted number of indels adjacent to the variant site. Not a major issue, since it's a very minor feature (one of the lowest-ranked feature importance).

* Added [linguistic sequence complexity (LC)](https://doi.org/10.1093/bioinformatics/18.5.679) as a feature: 80-bp window adjacent to and spanning the variant position. For adjacent, the lower value (between right and left) is retained. **Therefore, be careful for models trained before this release. The feature set has changed.**
* Fixed a bug for xgboost mode when training and prediction mode used different feature set.
* Changed the ada model file name to have "ada" in it.

* To invoke xgboost for somaticseq_parallel.py, do `--algorithm xgboost` before the `paired` or `single` option. The default is still `ada`.
* Set tree depth = 16 for ada because this seems optimal after internal benchmarking.
* Minor bug fixes and improvements (see docs for details).

seqc2_v1.1
* This is a special release for the somatic mutation working group of the SEQC2 consortium to establish a set of tumor-normal reference samples
* It is based on v2 of SomaticSeq, containing custom scripts with hard-coded sample names, etc.
* Corresponding docker image at lethalfang/somaticseq:seqc2_v1.1
* NOT intended for general use.

Fixed a bug in nucleotide change feature in training mode. T>C and only T>C base change was not annotated properly.

* Re-wrote in Python some somatic caller run script generators that were once written in bash, at utilities/dockered_pipelines/makeSomaticScripts.py.
* Fixed setup.py, even though running "setup.py install" is optional. You can still (always) run scripts from where you downloaded SomaticSeq.

* Fixed some bash scripts involved with single-sample multi-thread callers.
* vcfModifier/splitVcf.py to handle multi-allelic calls better for indels, and exclude complex variants that are technically not indels. We may handle them separately (e.g., variants like GCA>GATT) in a future release.

seqc2_v1.0
* This is a special release for a one-time project.
* It is based on v2 of SomaticSeq, containing project-specific custom scripts and sample names, etc.
* Corresponding docker image at lethalfang/somaticseq:seqc2_v1.0

* **Not intended for general use.**