Files in DKMS-LSL/dr2s
Dual redundant reference sequencing
.Rbuildignore
.gitignore
DESCRIPTION
DR2S.Rproj
LICENSE
NAMESPACE
NEWS.md
R/DR2S-class.R
R/DR2S-methods.R
R/DR2S-package.R
R/DR2S-utils.R
R/RcppExports.R
R/all-generics.R
R/callVariants.R
R/classes.R
R/config.R
R/configOpts.R
R/conseq.R
R/consmat.R
R/dists.R
R/log-config.R
R/mapInitSR.R
R/mapWrap.R
R/mapper.R
R/partitionLongreads.R
R/partitionShortreads.R
R/pileup.R
R/polymorphic-positions.R
R/postprocessScripts.R
R/report.R
R/samtools.R
R/sequtils.R
R/snp-matrix.R
R/utils.R
R/zzz.R
README.Rmd
README.md
inst/extSrc/minimap2
inst/extdata/HLAREF.fa
inst/testData/Illumina_sampled/sample3_A_MiSeq_1_sampled.fastq.gz
inst/testData/nanopore_sampled/sample3_A_nanopore_sampled.fastq.gz
man/DR2S.Rd
man/DR2S_.Rd
man/HapPart.Rd
man/InitDR2S.Rd
man/SNPmatrix.Rd
man/bampath.Rd
man/cache.Rd
man/checkAlignmentFile.Rd
man/checkHomopolymerCount.Rd
man/clear.Rd
man/conseq.Rd
man/consmat.Rd
man/consname.Rd
man/conspath.Rd
man/createDR2SConf.Rd
man/createIgvConfigs.Rd
man/createIgvJsFiles.Rd
man/createPWM.Rd
man/disambiguateVariant.Rd
man/dot-generateReferenceSequence.Rd
man/dot-getIdleCores.Rd
man/getSRPartitionScores.Rd
man/hammingDist.Rd
man/mapFinal.Rd
man/mapInit.Rd
man/mapIter.Rd
man/meta.Rd
man/partitionLongreads.Rd
man/partitionReads.Rd
man/partitionShortreads.Rd
man/pileup.Rd
man/plotDiagnosticAlignment.Rd
man/plotPartitionHistogram.Rd
man/plotPartitionHistogramMulti.Rd
man/plotPartitionTree.Rd
man/plotPileupBasecallFrequency.Rd
man/plotPileupCoverage.Rd
man/plotRadarPartition.Rd
man/polymorphicPositions.Rd
man/readDR2S.Rd
man/readDR2SConf.Rd
man/readMSA.Rd
man/readpath.Rd
man/readtype.Rd
man/reexports.Rd
man/refname.Rd
man/refpath.Rd
man/remapAlignment.Rd
man/report.Rd
man/reportCheckedConsensus.Rd
man/runrsubread.Rd
man/scoreHighestSR.Rd
man/stats.Rd
man/subSampleBam.Rd
man/tag.Rd
man/writeDR2SConf.Rd
man/writeMSA.Rd
src/RcppExports.cpp
src/cpphamming.cpp
src/cpppsdm.cpp
src/cpputils.cpp
src/symbols.rds
tests/testthat.R
tests/testthat/dr2s.rds
tests/testthat/helper_dr2sClass.R
tests/testthat/test_config.R
tests/testthat/test_consmat.R
tests/testthat/test_dr2sClass.R
tests/testthat/test_subsamplebam.R
tests/testthat/test_true.R
tests/testthat/test_utils.R
vignettes/DR2S.Rmd
