Files in jmonlong/sveval
SV evaluation
.Rbuildignore
.covrignore
.gitignore
.travis.yml
DESCRIPTION
Dockerfile
LICENSE
Makefile
NAMESPACE
R/RcppExports.R
R/annotateOl.R
R/annotateOl.bipartite.R
R/annotateOl.coverage.R
R/annotateOl.reciprocal.R
R/clusterSVs.R
R/countAlleles.R
R/evalOl.R
R/explore_eval_svs.R
R/extendSVwithSimpRep.R
R/filterSVs.R
R/findNocalls.R
R/freqAnnotate.R
R/ivg_sv.R
R/mergeHets.R
R/plot_perregion.R
R/plot_persize.R
R/plot_prcurve.R
R/plot_ranges.R
R/prepareOl.R
R/prf.R
R/readSVvcf.R
R/readSVvcf.multisamps.R
R/rmskAnnotate.R
R/stitchMergeHets.R
R/stitchSVs.R
R/subset_eval.R
R/svOverlap.R
R/sveval-package.R
R/svevalOl.R
R/wrapper.R
R/wrapper_mergetsvs.R
R/wrapper_sveval.R
README.md
docs/README.md
docs/explore_eval_svs.gif
docs/ivgsv.gif
docs/ivgsv_screenshot.jpg
docs/master.time.log
docs/methods-bipartite.Rmd
docs/methods-bipartite.md
docs/methods-bipartite_files/figure-gfm/bipartite-1.png
docs/methods-bipartite_files/figure-gfm/bipartite-2.png
docs/methods-bipartite_files/figure-gfm/readtests.del-1.png
docs/methods-bipartite_files/figure-gfm/splitfgt-1.png
docs/methods-bipartite_files/figure-gfm/splithom-1.png
docs/ol-cartoon.svg
docs/prepare-simple-repeat-track-from-ucsc.Rmd
docs/prepare-simple-repeat-track-from-ucsc.md
docs/rcpp.time.log
docs/simpleRepeat_GRCh37.bed.gz
docs/simpleRepeat_GRCh38.bed.gz
docs/sveval-manual.pdf
docs/time.R
install.R
man/aldist.Rd
man/annotateOl.Rd
man/annotateOl.bipartite.Rd
man/annotateOl.coverage.Rd
man/annotateOl.reciprocal.Rd
man/clusterSVs.Rd
man/countAlleles.Rd
man/evalOl.Rd
man/explore_eval_svs.Rd
man/extendSVwithSimpRep.Rd
man/filterSVs.Rd
man/findNocalls.Rd
man/freqAnnotate.Rd
man/ivg_sv.Rd
man/mergeHets.Rd
man/merge_ac_svsites_cpp.Rd
man/merge_gq_svsites_cpp.Rd
man/plot_perregion.Rd
man/plot_persize.Rd
man/plot_prcurve.Rd
man/plot_ranges.Rd
man/prepareOl.Rd
man/prf.Rd
man/readSVvcf.Rd
man/readSVvcf.multisamps.Rd
man/read_vcf_cpp.Rd
man/read_vcf_multisamps_cpp.Rd
man/rmskAnnotate.Rd
man/stitchMergeHets.Rd
man/stitchSVs.Rd
man/subset_eval.Rd
man/svOverlap.Rd
man/sveval-package.Rd
man/svevalOl.Rd
man/wrapper.Rd
man/wrapper_mergetsvs.Rd
man/wrapper_sveval.Rd
snakemake/README.md
snakemake/Snakefile
snakemake/config.example.yaml
snakemake/config.yaml
src/.gitignore
src/RcppExports.cpp
src/aldist.cpp
src/edlib.cpp
src/edlib.h
src/gzstream.cpp
src/gzstream.h
src/merge-ac-svsites.cpp
src/read-vcf-multisamps.cpp
src/read-vcf.cpp
src/utils.cpp
src/utils.h
tests/calls.s0.vcf
tests/delgenotype.bed
tests/delly.vcf
tests/delly.vcf.bgz
tests/delly.vcf.gz
tests/empty.vcf
tests/ex.gq.vcf
tests/example-calls.vcf
tests/example-truth.vcf
tests/make-test-data.R
tests/testthat.R
tests/testthat/test_freqannotate.R
tests/testthat/test_graphs.R
tests/testthat/test_multisamps.R
tests/testthat/test_nocalls.R
tests/testthat/test_overlap.R
tests/testthat/test_readvcf.R
tests/testthat/test_svclustering.R
tests/testthat/test_svevalol.R
tests/testthat/test_svevalol_bipartite.R
tests/testthat/test_svevalol_geno.R
tests/testthat/test_svevalol_geno_example.R
tests/truth.refalt.vcf
tests/truth.symb.vcf
