├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── asgal ├── docker ├── Dockerfile └── asgal-docker.sh ├── docs ├── CNAME ├── _config.yml ├── _data │ └── navigation.yml ├── citation.bib ├── documentation.md ├── examples.md ├── experiments.md ├── genomewide.md └── index.md ├── example ├── .gitignore ├── events.events ├── input.tar.gz └── sashimi.png ├── paper └── experiments │ ├── RealData │ ├── Snakefile │ ├── config.yaml │ └── setupData.sh │ └── SimulatedData │ ├── Snakefile │ ├── config.yaml │ ├── getTools.sh │ ├── scripts │ ├── addUniqueID.py │ ├── cleanAndSplitSample.sh │ ├── combineSame.py │ ├── formatAsta.py │ ├── moveAnnos.py │ ├── splitAnnotation.py │ ├── splitReference.py │ └── transcriptsRemover.py │ ├── setupData.sh │ └── tools │ ├── alnsAnalysis │ └── checkAlignments.py │ ├── comparaTHOR │ ├── comparANNOT.py │ └── comparaTHOR.py │ ├── concat_comparisons.py │ ├── cutAnnotations.py │ ├── fixFastaTranscr.py │ ├── multipleFieldSelection.py │ ├── splitSalmonBAM.py │ └── split_file.R ├── scripts ├── .gitignore ├── BitVector.py ├── SplicingGraph.py ├── detectEvents.py ├── formatSAM.py └── utils.py ├── src ├── MEMsGraph.cpp ├── MEMsGraph.hpp ├── SpliceAwareAligner.cpp ├── SplicingGraph.cpp ├── SplicingGraph.hpp ├── bMEM.cpp ├── bMEM.hpp ├── kseq.h ├── utils.cpp └── utils.hpp └── target.mk /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlgoLab/galig/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlgoLab/galig/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlgoLab/galig/HEAD/Makefile 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