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.**

* Fixed a bug introduced in v3.0.1 that caused the program to handle .vcf.gz files incorrectly.
* Incorporated Platypus into paired mode.
* When splitting MuTect2 files into SNV and INDEL, make sure either the ref base or the alt base (but not both) consists of a single base, i.e., discarding complex variants like GCAA>GCT.

Fixed a bug that was introduced in v3.0.0, that did not handle Strelka and LoFreq indel files correctly.

Made SomaticSeq extendable as a python library.
See docs/Manual.pdf for details.

* Allow parallel processing through somaticseq_parallel.py.
* The wrapper scripts written in bash script (i.e., SomaticSeq.Wrapper.sh and ssSomaticSeq.Wrapper.sh) are replaced by somaticseq/run_somaticseq.py, though they're still kept for backward-compatibility.

Fixed a bug in the ssSomaticSeq.Wrapper.sh script (single-sample mode), where the SNV algorithm weren't looking for SNV VCF files during merging when using utilities/getUniqueVcfPositions.py, causing empty SNV files. For previous commands (invoking --gatk for CombineVariants), the results have never changed.