Special release for SEQC2 special project

• 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 the TA2CG variable in R script

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

Improved installation script

• 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.

minor maintenance release

• 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.

Special release for one-time project

• 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.

bug fix and add support for platypus

• 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.

bug fix

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

version 3 release

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

Refactored codes and enabled parallel processing

• 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.

Bug fix for single-sample mode

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.