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
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inst/testData/ID14984936/mapFinal/LRA.pacbio.minimap.A.default50MAPQ.sorted.sampled.bam
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inst/testData/ID14984936/mapFinal/LRB.pacbio.minimap.B.default50MAPQ.sorted.sampled.bam
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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
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inst/testData/ID14984936/mapFinal/SRB.illumina.bwamem..default50MAPQ.sorted.sampled.bam
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inst/testData/ID14984936/mapInit/A/consensus.mapIter2.pacbio.minimap.consensus.mapIter1.pacbio.minimap.mapIter0.A.sorted.A.sorted.fa
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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
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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
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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
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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
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inst/testData/ID14984936/refine/LRB.pacbio.minimap.B.default.sorted.bam
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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
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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
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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
