Files in DKMS-LSL/dr2s

Dual redundant reference sequencing

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 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 tests/testthat.R 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