├── .gitmodules ├── .travis.yml ├── Makefile ├── README.md ├── pipeline ├── Snakefile ├── annotation │ ├── config.json │ ├── config.sh │ └── helper_scripts │ │ ├── closestGene.sh │ │ └── isCoding.sh ├── config.json ├── config.sh └── target_names.txt ├── src ├── annotate.cpp ├── annotate.hpp ├── chain.cpp ├── chain.hpp ├── cigar.cpp ├── cigar.hpp ├── errors.cpp ├── errors.hpp ├── main.cpp ├── split.cpp ├── split.hpp ├── varcall.cpp └── varcall.hpp └── utils ├── dotPlot.sh ├── embossPlot.sh └── plotDot.R /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/.gitmodules -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/.travis.yml -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/README.md -------------------------------------------------------------------------------- /pipeline/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/pipeline/Snakefile -------------------------------------------------------------------------------- /pipeline/annotation/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/pipeline/annotation/config.json -------------------------------------------------------------------------------- /pipeline/annotation/config.sh: -------------------------------------------------------------------------------- 1 | module load bedtools/latest -------------------------------------------------------------------------------- /pipeline/annotation/helper_scripts/closestGene.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/pipeline/annotation/helper_scripts/closestGene.sh -------------------------------------------------------------------------------- /pipeline/annotation/helper_scripts/isCoding.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/pipeline/annotation/helper_scripts/isCoding.sh -------------------------------------------------------------------------------- /pipeline/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/pipeline/config.json -------------------------------------------------------------------------------- /pipeline/config.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/pipeline/config.sh -------------------------------------------------------------------------------- /pipeline/target_names.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/pipeline/target_names.txt -------------------------------------------------------------------------------- /src/annotate.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/annotate.cpp -------------------------------------------------------------------------------- /src/annotate.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/annotate.hpp -------------------------------------------------------------------------------- /src/chain.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/chain.cpp -------------------------------------------------------------------------------- /src/chain.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/chain.hpp -------------------------------------------------------------------------------- /src/cigar.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/cigar.cpp -------------------------------------------------------------------------------- /src/cigar.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/cigar.hpp -------------------------------------------------------------------------------- /src/errors.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/errors.cpp -------------------------------------------------------------------------------- /src/errors.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/errors.hpp -------------------------------------------------------------------------------- /src/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/main.cpp -------------------------------------------------------------------------------- /src/split.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/split.cpp -------------------------------------------------------------------------------- /src/split.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/split.hpp -------------------------------------------------------------------------------- /src/varcall.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/varcall.cpp -------------------------------------------------------------------------------- /src/varcall.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/src/varcall.hpp -------------------------------------------------------------------------------- /utils/dotPlot.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/utils/dotPlot.sh -------------------------------------------------------------------------------- /utils/embossPlot.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/utils/embossPlot.sh -------------------------------------------------------------------------------- /utils/plotDot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zeeev/DASVC/HEAD/utils/plotDot.R --------------------------------------------------------------------------------