Files in gschofl/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/MergeEnv-class.R R/MergeEnv-methods.R R/RcppExports.R R/all-generics.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/polish.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/extdata/HLAREF.fa
inst/scripts/barcodes2sampleid.sh
inst/scripts/dr2s.R
inst/testData/ID14984936/.plots/plot.MapFinal.svg
inst/testData/ID14984936/.plots/plot.MapInit.svg
inst/testData/ID14984936/.plots/plot.MapIter.svg
inst/testData/ID14984936/.plots/plot.Partition.svg
inst/testData/ID14984936/.plots/plot.Sequence.svg
inst/testData/ID14984936/.pplib/checkConsensus.R
inst/testData/ID14984936/.pplib/igvAmapIter.win.xml
inst/testData/ID14984936/.pplib/igvAmapIter.xml
inst/testData/ID14984936/.pplib/igvArefine.win.xml
inst/testData/ID14984936/.pplib/igvArefine.xml
inst/testData/ID14984936/.pplib/igvBmapIter.win.xml
inst/testData/ID14984936/.pplib/igvBmapIter.xml
inst/testData/ID14984936/.pplib/igvBrefine.win.xml
inst/testData/ID14984936/.pplib/igvBrefine.xml
inst/testData/ID14984936/.pplib/igvInitmapInit.win.xml
inst/testData/ID14984936/.pplib/igvInitmapInit.xml
inst/testData/ID14984936/.pplib/remapA.R inst/testData/ID14984936/.pplib/remapB.R inst/testData/ID14984936/.pplib/reportCheckedConsensus.R
inst/testData/ID14984936/DR2S.pacbio.minimap.rds
inst/testData/ID14984936/DR2S_run.info
inst/testData/ID14984936/checked/aln.pacbio.minimap.html.fa
inst/testData/ID14984936/checked/aln.pacbio.minimap.html.html
inst/testData/ID14984936/checked/hapA.pacbio.minimap.fa
inst/testData/ID14984936/checked/hapB.pacbio.minimap.fa
inst/testData/ID14984936/mapFinal/LRA.pacbio.minimap.A.default50MAPQ.sorted.bam
inst/testData/ID14984936/mapFinal/LRA.pacbio.minimap.A.default50MAPQ.sorted.bam.bai
inst/testData/ID14984936/mapFinal/LRA.pacbio.minimap.A.default50MAPQ.sorted.sampled.bam
inst/testData/ID14984936/mapFinal/LRA.pacbio.minimap.A.default50MAPQ.sorted.sampled.bam.bai
inst/testData/ID14984936/mapFinal/LRB.pacbio.minimap.B.default50MAPQ.sorted.bam
inst/testData/ID14984936/mapFinal/LRB.pacbio.minimap.B.default50MAPQ.sorted.bam.bai
inst/testData/ID14984936/mapFinal/LRB.pacbio.minimap.B.default50MAPQ.sorted.sampled.bam
inst/testData/ID14984936/mapFinal/LRB.pacbio.minimap.B.default50MAPQ.sorted.sampled.bam.bai
inst/testData/ID14984936/mapFinal/SRA.illumina.bwamem..default50MAPQ.sorted.bam
inst/testData/ID14984936/mapFinal/SRA.illumina.bwamem..default50MAPQ.sorted.bam.bai
inst/testData/ID14984936/mapFinal/SRA.illumina.bwamem..default50MAPQ.sorted.sampled.bam
inst/testData/ID14984936/mapFinal/SRA.illumina.bwamem..default50MAPQ.sorted.sampled.bam.bai
inst/testData/ID14984936/mapFinal/SRB.illumina.bwamem..default50MAPQ.sorted.bam
inst/testData/ID14984936/mapFinal/SRB.illumina.bwamem..default50MAPQ.sorted.bam.bai
inst/testData/ID14984936/mapFinal/SRB.illumina.bwamem..default50MAPQ.sorted.sampled.bam
inst/testData/ID14984936/mapFinal/SRB.illumina.bwamem..default50MAPQ.sorted.sampled.bam.bai
inst/testData/ID14984936/mapFinal/consensus.mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.A.sorted.A.sorted.fa
inst/testData/ID14984936/mapFinal/consensus.mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.A.sorted.A.sorted.fa.fai
inst/testData/ID14984936/mapFinal/consensus.mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.B.sorted.B.sorted.fa
inst/testData/ID14984936/mapInit/A/consensus.mapIter.0.A.fa
inst/testData/ID14984936/mapInit/A/consensus.mapIter1.pacbio.minimap.mapIter0.A.sorted.fa
inst/testData/ID14984936/mapInit/A/consensus.mapIter1.pacbio.minimap.mapIter0.A.sorted.fa.fai
inst/testData/ID14984936/mapInit/A/consensus.mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.A.sorted.A.sorted.fa
inst/testData/ID14984936/mapInit/A/consensus.mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.A.sorted.A.sorted.fa.fai
inst/testData/ID14984936/mapInit/A/mapIter1.pacbio.minimap.mapIter0.A.sorted.bam
inst/testData/ID14984936/mapInit/A/mapIter1.pacbio.minimap.mapIter0.A.sorted.bam.bai
inst/testData/ID14984936/mapInit/A/mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.A.sorted.A.sorted.bam
inst/testData/ID14984936/mapInit/A/mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.A.sorted.A.sorted.bam.bai
inst/testData/ID14984936/mapInit/B/consensus.mapIter.0.B.fa
inst/testData/ID14984936/mapInit/B/consensus.mapIter1.pacbio.minimap.mapIter0.B.sorted.fa
inst/testData/ID14984936/mapInit/B/consensus.mapIter1.pacbio.minimap.mapIter0.B.sorted.fa.fai
inst/testData/ID14984936/mapInit/B/consensus.mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.B.sorted.B.sorted.fa
inst/testData/ID14984936/mapInit/B/consensus.mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.B.sorted.B.sorted.fa.fai
inst/testData/ID14984936/mapInit/B/mapIter1.pacbio.minimap.mapIter0.B.sorted.bam
inst/testData/ID14984936/mapInit/B/mapIter1.pacbio.minimap.mapIter0.B.sorted.bam.bai
inst/testData/ID14984936/mapInit/B/mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.B.sorted.B.sorted.bam
inst/testData/ID14984936/mapInit/B/mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.B.sorted.B.sorted.bam.bai
inst/testData/ID14984936/mapInit/HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.bam
inst/testData/ID14984936/mapInit/HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.bam.bai
inst/testData/ID14984936/mapInit/HLA-A_01_01_01_01.ref.fa
inst/testData/ID14984936/mapInit/HLA-A_01_01_01_01.ref.fa.fai
inst/testData/ID14984936/mapInit/Init.consensus.2Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.fa
inst/testData/ID14984936/mapInit/Init.consensus.2Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.fa.fai
inst/testData/ID14984936/mapInit/Init.consensus.2Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.bam
inst/testData/ID14984936/mapInit/Init.consensus.2Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.bam.bai
inst/testData/ID14984936/mapInit/Init.consensus.2Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.sampled.bam
inst/testData/ID14984936/mapInit/Init.consensus.2Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.sampled.bam.bai
inst/testData/ID14984936/mapInit/Init.consensus.2Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.pacbio.minimap..default50MAPQ.sorted.bam
inst/testData/ID14984936/mapInit/Init.consensus.2Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.pacbio.minimap..default50MAPQ.sorted.bam.bai
inst/testData/ID14984936/mapInit/Init.consensus.2Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.pacbio.minimap..default50MAPQ.sorted.sampled.bam
inst/testData/ID14984936/mapInit/Init.consensus.2Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.pacbio.minimap..default50MAPQ.sorted.sampled.bam.bai
inst/testData/ID14984936/mapInit/Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.fa
inst/testData/ID14984936/mapInit/Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.fa.fai
inst/testData/ID14984936/mapInit/Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.bam
inst/testData/ID14984936/mapInit/Init.consensus.HLA-A_01_01_01_01.illumina.bwamem..default50MAPQ.sorted.illumina.bwamem..default50MAPQ.sorted.bam.bai
inst/testData/ID14984936/mapIter/A/ID14984936_S36_L001_R1_001.A.fastq.gz
inst/testData/ID14984936/mapIter/A/ID14984936_S36_L001_R2_001.A.fastq.gz
inst/testData/ID14984936/mapIter/A/consensus.mapIter.0.A.fa
inst/testData/ID14984936/mapIter/A/consensus.mapIter.0.A.fa.fai
inst/testData/ID14984936/mapIter/A/hap.A.pacbio.minimap.lim4412.66138579462.n38.fastq.gz
inst/testData/ID14984936/mapIter/B/ID14984936_S36_L001_R1_001.B.fastq.gz
inst/testData/ID14984936/mapIter/B/ID14984936_S36_L001_R2_001.B.fastq.gz
inst/testData/ID14984936/mapIter/B/consensus.mapIter.0.B.fa
inst/testData/ID14984936/mapIter/B/consensus.mapIter.0.B.fa.fai
inst/testData/ID14984936/mapIter/B/hap.B.pacbio.minimap.lim4473.94834948621.n21.fastq.gz
inst/testData/ID14984936/partition.fa.html
inst/testData/ID14984936/plot.MapFinal.pdf inst/testData/ID14984936/plot.MapInit.pdf inst/testData/ID14984936/plot.MapIter.pdf inst/testData/ID14984936/plot.Partition.pdf inst/testData/ID14984936/plot.Sequence.pdf
inst/testData/ID14984936/refine/LRA.pacbio.minimap.A.default.sorted.bam
inst/testData/ID14984936/refine/LRA.pacbio.minimap.A.default.sorted.bam.bai
inst/testData/ID14984936/refine/LRA.pacbio.minimap.A.default.sorted.sampled.bam
inst/testData/ID14984936/refine/LRA.pacbio.minimap.A.default.sorted.sampled.bam.bai
inst/testData/ID14984936/refine/LRB.pacbio.minimap.B.default.sorted.bam
inst/testData/ID14984936/refine/LRB.pacbio.minimap.B.default.sorted.bam.bai
inst/testData/ID14984936/refine/LRB.pacbio.minimap.B.default.sorted.sampled.bam
inst/testData/ID14984936/refine/LRB.pacbio.minimap.B.default.sorted.sampled.bam.bai
inst/testData/ID14984936/refine/SRA.illumina.bwamem.A.default.sorted.bam.bai
inst/testData/ID14984936/refine/SRB.illumina.bwamem.B.default.sorted.bam.bai
inst/testData/ID14984936/refine/hapA.pacbio.minimap.polished.fa
inst/testData/ID14984936/refine/hapA.pacbio.minimap.polished.fa.fai
inst/testData/ID14984936/refine/hapA.pacbio.minimap.refined.fa
inst/testData/ID14984936/refine/hapA.pacbio.minimap.refined.fa.fai
inst/testData/ID14984936/refine/hapB.pacbio.minimap.polished.fa
inst/testData/ID14984936/refine/hapB.pacbio.minimap.polished.fa.fai
inst/testData/ID14984936/refine/refine.SRA.pacbio.bwamem.illumina.bwamem.A.A1B4O2default.sorted.bam
inst/testData/ID14984936/refine/refine.SRA.pacbio.bwamem.illumina.bwamem.A.A1B4O2default.sorted.bam.bai
inst/testData/ID14984936/refine/refine.SRA.pacbio.bwamem.illumina.bwamem.A.A1B4O2default.sorted.sampled.bam
inst/testData/ID14984936/refine/refine.SRA.pacbio.bwamem.illumina.bwamem.A.A1B4O2default.sorted.sampled.bam.bai
inst/testData/ID14984936/refine/refine.SRB.pacbio.bwamem.illumina.bwamem.B.A1B4O2default.sorted.bam
inst/testData/ID14984936/refine/refine.SRB.pacbio.bwamem.illumina.bwamem.B.A1B4O2default.sorted.bam.bai
inst/testData/ID14984936/refine/refine.SRB.pacbio.bwamem.illumina.bwamem.B.A1B4O2default.sorted.sampled.bam
inst/testData/ID14984936/refine/refine.SRB.pacbio.bwamem.illumina.bwamem.B.A1B4O2default.sorted.sampled.bam.bai
inst/testData/ID14984936/report/mapfinal.A.pacbio.minimap.unchecked.fa
inst/testData/ID14984936/report/mapfinal.B.pacbio.minimap.unchecked.fa
inst/testData/ID14984936/report/mapfinal.aln.pacbio.minimap.checked.psa
inst/testData/ID14984936/report/mapfinal.aln.pacbio.minimap.unchecked.fa
inst/testData/ID14984936/report/mapfinal.aln.pacbio.minimap.unchecked.html
inst/testData/ID14984936/report/mapfinal.aln.pacbio.minimap.unchecked.psa
inst/testData/ID14984936/report/problems.pacbio.minimap.tsv
inst/testData/ID14984936/runIGV_mapInit.sh
inst/testData/ID14984936/runIGV_mapIter.sh
inst/testData/ID14984936/runIGV_refine.sh
inst/testData/ID14984936/run_checkConsensus.sh
inst/testData/ID14984936/run_remapA.sh
inst/testData/ID14984936/run_remapB.sh
inst/testData/ID14984936/run_reportCheckedConsensus.sh
inst/testData/ID14984936/win/runIGV_mapInit.bat
inst/testData/ID14984936/win/runIGV_mapIter.bat
inst/testData/ID14984936/win/runIGV_refine.bat
inst/testData/Illumina/ID14984936_S36_L001_R1_001.fastq.gz
inst/testData/Illumina/ID14984936_S36_L001_R2_001.fastq.gz
inst/testData/Sequel/ID14984936.lbc36.mod.fastq.gz
inst/testData/prob
man/DR2S.Rd man/DR2S_.Rd man/HapPart.Rd man/InitDR2S.Rd man/MergeEnv.Rd man/MergeEnv_.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/polish.Rd man/polymorphicPositions.Rd man/readDR2S.Rd man/readDR2SConf.Rd man/readMSA.Rd man/readpath.Rd man/readtype.Rd man/reexports.Rd man/refineAlignment.Rd man/refname.Rd man/refpath.Rd man/report.Rd man/reportCheckedConsensus.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
gschofl/DR2S documentation built on Dec. 19, 2018, 8:04 a.m.