Somaticseq

*\* Typo in mutect input variable, so the wrapper script did not see mutect even when it was provided.
*\* Used the wrong file name for SSeq_merged.vcf2tsv.py in the script.

Updated the release due to a typo in the wrapper script (i.e., mutect_dir instead of mutect_vcf)

SomaticSeq now handles different variant calls at the same chromosome coordinate. The input VCF file can either have multiple lines of the same coordinate, or have multiple calls in the ALT column separated by a comma (e.g., A,G).
Previously, it assumed one single variant call for each position. If there are multiple ALT calls, only most abundant ALT call was considered.

1) Allow long options (e.g., --mutect | -M ) for the SomaticSeq.Wrapper.sh script. The original script is renamed SomaticSeq.Wrapper.1.sh, which will be removed after we make sure there is no bug in the new script.
2) The VCF files generated will have version number written into the header.

Handle cases when a called variant position is within 20 base pairs of the ends of the reference sequence.

When and only when SomaticSeq.Wrapper.sh is not in training or predicting mode, it will fall back into a naive consensus mode:
- A call agreed upon by over 50% of the callers will be labeled PASS
- A call agreed upon by at least 1/3, but no more than 50% of the callers, will be labeled LowQual.
- The remaining will be labeled REJECT.

Caller consensus is only invoked if there is no trained classifier specified or ground truth file to train a classifier.