Indel model improvement

• SSeq_merged.vcf2tsv.py can now accept pileup files to extract read depth and DP4 (reference forward, reference reverse, alternate forward, and alternate reverse) information (mainly for indels). Previously, that information can only be extracted from SAMtools VCF. Since the SAMtools or HaplotypeCaller generated VCFs hardly contain any indel information, this option improves the indel model. The SomaticSeq.Wrapper.sh script is modified accordingly.
• Extract mapping quality (MQ) from VarDict output if this information cannot be found in SAMtools VCF (also mostly benefits the indel model).
• Indel length now positive for insertions and negative for deletions, instead of using the absolute value previously.

Improved automation

Automate both model training and mutation prediction. Training or prediction mode based on files supplied. No significant change from previous version.

Initial release of SomaticSeq

This version was used for the results in the SomaticSeq manuscript.