API for DKMS-LSL/dr2s
Dual redundant reference sequencing
| Global functions | |
|---|---|
| %>% | Man page |
| .PWMscore | Source code |
| .ambiguousPositions | Source code |
| .ambiguousPositions.NULL | Source code |
| .ambiguousPositions.consmat | Source code |
| .ambiguousPositions.pileup | Source code |
| .associationMatrix | Source code |
| .bamSortIndex | Source code |
| .browseAlign | Source code |
| .browseSeqs | Source code |
| .callVariants | Source code |
| .camelCasify | Source code |
| .capitalise | Source code |
| .checkCoverage | Source code |
| .collapseHomopolymers | Source code |
| .collapsePairLines_ | Source code |
| .collectPileupParams | Source code |
| .confLog | Source code |
| .coordRadar | Source code |
| .coverage | Source code |
| .cropOutdir | Source code |
| .cropPath | Source code |
| .dirCreateIfNotExists | Source code |
| .distributeGaps | Source code |
| .equaliseConsmat | Source code |
| .expandAllele | Source code |
| .expandLongreadConsmat | Source code |
| .extractFastq | Source code |
| .extractIdsFromMat | Source code |
| .extractInsertion | Source code |
| .extractVariant_ | Source code |
| .fileDeleteIfExists | Source code |
| .filterReads | Source code |
| .filterVariant | Source code |
| .findChimeric | Source code |
| .findMostDistantPwm | Source code |
| .finishCn1 | Source code |
| .fragmentReads | Source code |
| .generateMappingCommands | Source code |
| .generateReferenceSequence | Man page Source code |
| .getAmbigPositions | Source code |
| .getClusts | Source code |
| .getGapErrorBackground | Source code |
| .getIdleCores | Man page Source code |
| .getInsertions | Source code |
| .getMinLenClust | Source code |
| .getModeValue | Source code |
| .getScores | Source code |
| .getSeqsFromMat | Source code |
| .getUpdatedSeqs | Source code |
| .getVariants | Source code |
| .hasCommand | Source code |
| .ipdHla | Source code |
| .ipdKir | Source code |
| .makeAmbigConsensus_ | Source code |
| .makeOpts | Source code |
| .makeProbConsensus_ | Source code |
| .makeSimpleConsensus_ | Source code |
| .mapSoftclip | Source code |
| .mat2rle | Source code |
| .msaFromBam | Source code |
| .noRefMatch | Source code |
| .normaliseLocus | Source code |
| .normaliseUtrLength | Source code |
| .onLoad | Source code |
| .optimalPartitionLimits | Source code |
| .pickReads | Source code |
| .pickTopXReads | Source code |
| .pileupFindInsertionPositions_ | Source code |
| .pileupGetInsertions_ | Source code |
| .pileupIncludeInsertions | Source code |
| .pwmDiff | Source code |
| .read_score | Source code |
| .reportMap_ | Source code |
| .selectAssociatedPolymorphicPositions | Source code |
| .seq2rle | Source code |
| .setRunstats | Source code |
| .suppressGaps_ | Source code |
| .trimPolymorphicEnds | Source code |
| .trimSoftclippedEnds | Source code |
| .trimToRefLen | Source code |
| .variant | Source code |
| .walkVariants | Source code |
| .writeCheckConsensus | Source code |
| .writeConseq | Source code |
| .writeRemapAlignments | Source code |
| .writeReportCheckedConsensus | Source code |
| CLS | Source code |
| CLS.HapPart | Man page Source code |
| CODE_MAP | Source code |
| CODE_PATTERN | Source code |
| COL_PATTERN | Source code |
| Consmat_ | Source code |
| DNA_BASES | Source code |
| DNA_PROB | Source code |
| DR2S | Man page |
| DR2S_ | Man page |
| HLA_LOCI | Source code |
| HTR | Source code |
| HTR.HapPart | Man page Source code |
| HapPart | Man page Source code |
| InitDR2S | Man page Source code |
| InitDR2S.DR2Sconf | Source code |
| K | Source code |
| K.HapPart | Man page Source code |
| KIR_LOCI | Source code |
| LR_PIPELINE | Source code |
| MANDATORY_CONF_FIELDS | Source code |
| MANDATORY_OPTS | Source code |
| MapList_ | Source code |
| NUCCOL | Source code |
| OC | Source code |
| OC.HapPart | Man page Source code |
| ORDERED_CONF_FIELDS | Source code |
| PARTCOL | Source code |
| POLISH_RANGE | Source code |
| PRT | Source code |
| PRT.HapPart | Man page Source code |
| PSDM | Source code |
| PWM | Source code |
| PWM.HapPart | Man page Source code |
| Pileup_ | Source code |
| SCR | Source code |
| SCR.HapPart | Man page Source code |
| SNP | Source code |
| SNP.HapPart | Man page Source code |
| SNPmatrix | Man page Source code |
| SQS | Source code |
| SQS.HapPart | Man page Source code |
| SR_PIPELINE | Source code |
| VALID_DNA | Source code |
| `%+%` | Source code |
| `%.%` | Source code |
| `%<<%` | Source code |
| `%|ch|%` | Source code |
| `%|na|%` | Source code |
| `%||%` | Source code |
| `CLS<-.HapPart` | Source code |
| `CLS<-` | Source code |
| `HTR<-.HapPart` | Source code |
| `HTR<-` | Source code |
| `K<-.HapPart` | Source code |
| `K<-` | Source code |
| `OC<-.HapPart` | Source code |
| `OC<-` | Source code |
| `PRT<-.HapPart` | Source code |
| `PRT<-` | Source code |
| `PWM<-.HapPart` | Source code |
| `PWM<-` | Source code |
| `SCR<-.HapPart` | Source code |
| `SCR<-` | Source code |
| `SNP<-.HapPart` | Source code |
| `SNP<-` | Source code |
| `SQS<-.HapPart` | Source code |
| `SQS<-` | Source code |
| `[.HapPart` | Source code |
| `[.consmat` | Source code |
| `[<-.consmat` | Source code |
| `consmat<-.pileup` | Source code |
| `consmat<-` | Source code |
| `indelRate<-.pileup` | Source code |
| `indelRate<-` | Source code |
| `ins<-.consmat` | Source code |
| `ins<-` | Source code |
| `mcoef<-.HapPart` | Source code |
| `mcoef<-` | Source code |
| `n<-.consmat` | Source code |
| `n<-` | Source code |
| `offsetBases<-.consmat` | Source code |
| `offsetBases<-` | Source code |
| `readfile<-.pileup` | Source code |
| `readfile<-` | Source code |
| `reads<-.pileup` | Source code |
| `reads<-` | Source code |
| as.data.frame.consmat | Source code |
| as.matrix.consmat | Source code |
| bampath | Man page Source code |
| bampath.MapList | Source code |
| bampath.pileup | Source code |
| bwamemCmd | Source code |
| cache | Man page Source code |
| cache.DR2S | Source code |
| checkAlignmentFile | Man page Source code |
| checkCovGaps | Source code |
| checkHomopolymerCount | Man page Source code |
| clear | Man page Source code |
| clear.DR2S | Source code |
| colon | Source code |
| comma | Source code |
| compact | Source code |
| conseq | Man page Source code |
| conseq.matrix | Source code |
| conseq.pileup | Source code |
| consmat | Man page Source code |
| consmat.MapList | Source code |
| consmat.consmat | Source code |
| consmat.matrix | Source code |
| consmat.pileup | Source code |
| consmat.tbl_df | Source code |
| consmat<- | Man page |
| consname | Man page Source code |
| consname.MapList | Source code |
| conspath | Man page Source code |
| conspath.MapList | Source code |
| contractSeqs | Source code |
| cpp_PSDM | Source code |
| cpp_hamming | Source code |
| cpp_polymorphicPositions | Source code |
| cpp_top2Cols | Source code |
| createDR2SConf | Man page Source code Source code |
| createIgvConfigs | Man page Source code |
| createIgvJsFiles | Man page Source code |
| createPWM | Man page Source code |
| disambiguateVariant | Man page Source code |
| dot | Source code |
| editor | Source code |
| expandDR2SConf | Source code |
| extractAmbigLetters | Source code |
| findReads | Source code |
| findRef | Source code |
| getCl | Source code |
| getSRPartitionScores | Man page Source code |
| hammingDist | Man page Source code |
| in.seq | Source code |
| incr | Source code |
| incr.indenter | Source code |
| indelRate | Man page Source code |
| indelRate.pileup | Source code |
| indelRate<- | Man page |
| indentation | Source code |
| initialiseDR2S | Source code |
| ins | Man page Source code |
| ins.consmat | Source code |
| ins<- | Man page |
| is.freq | Man page Source code |
| is.freq.consmat | Source code |
| litArrows | Source code |
| litQuote | Source code |
| lvl | Source code |
| lvl.indenter | Source code |
| mapFinal | Man page Source code |
| mapFinal.DR2S | Source code |
| mapInit | Man page Source code |
| mapInit.DR2S | Source code |
| mapInitSR | Source code |
| mapIter | Man page Source code |
| mapIter.DR2S | Source code |
| mapReads | Source code |
| mcoef | Source code |
| mcoef.HapPart | Man page Source code |
| mergeList | Source code |
| meta | Man page Source code |
| meta.MapList | Source code |
| meta.pileup | Source code |
| minimapCmd | Source code |
| n | Man page Source code |
| n.consmat | Source code |
| n<- | Man page |
| normaliseDR2SConf | Source code |
| normaliseLongreads | Source code |
| normaliseOpts | Source code |
| normaliseShortreads | Source code |
| offsetBases | Man page Source code |
| offsetBases.consmat | Source code |
| offsetBases<- | Man page |
| optstring | Source code |
| partition | Source code |
| partition.HapPart | Source code |
| partitionLongreads | Man page Source code |
| partitionLongreads.DR2S | Source code |
| partitionReads | Man page Source code |
| partitionShortreads | Man page Source code |
| partitionShortreads.DR2S | Source code |
| pileup | Man page Source code |
| plotDiagnosticAlignment | Man page Source code |
| plotPartitionHistogram | Man page Source code |
| plotPartitionHistogramMulti | Man page Source code |
| plotPartitionTree | Man page Source code |
| plotPileupBasecallFrequency | Man page Source code |
| plotPileupCoverage | Man page Source code |
| plotRadarPartition | Man page Source code |
| polymorphicPositions | Man page Source code |
| polymorphicPositions.consmat | Source code |
| polymorphicPositions.pileup | Source code |
| print.DR2Sconf | Source code |
| print.HapList | Source code |
| print.HapPart | Source code |
| print.MapList | Source code |
| print.PartList | Source code |
| print.consmat | Source code |
| print.pileup | Source code |
| print.variant | Source code |
| print.variantList | Source code |
| readDR2S | Man page Source code |
| readDR2SConf | Man page Source code |
| readMSA | Man page Source code |
| readPairFile | Source code |
| readfile | Man page Source code |
| readfile.pileup | Source code |
| readfile<- | Man page |
| readpath | Man page Source code |
| readpath.MapList | Source code |
| reads | Man page Source code |
| reads.pileup | Source code |
| reads<- | Man page |
| readtype | Man page Source code |
| readtype.MapList | Source code |
| readtype.pileup | Source code |
| reexports | Man page |
| refname | Man page Source code |
| refname.MapList | Source code |
| refname.pileup | Source code |
| refpath | Man page Source code |
| refpath.MapList | Source code |
| refpath.pileup | Source code |
| remapAlignment | Man page Source code |
| remapAndReport | Source code |
| report | Man page Source code |
| report.DR2S | Source code |
| reportCheckedConsensus | Man page Source code |
| rescale | Source code |
| runbwamem | Source code |
| runminimap | Source code |
| runrsubread | Man page Source code |
| sambambaSubSample | Source code |
| scoreHighestSR | Man page Source code |
| semicolon | Source code |
| stats | Man page Source code |
| stats.MapList | Source code |
| stats.pileup | Source code |
| strip | Source code |
| stripIndel | Source code |
| strsplit1 | Source code |
| strsplitN | Source code |
| subSampleBam | Man page Source code |
| tag | Man page Source code |
| tag.MapList | Source code |
| underscore | Source code |
| updateDR2SConf | Source code |
| validateOpts | Source code |
| wrap | Source code |
| writeDR2SConf | Man page Source code |
| writeMSA | Man page Source code |
| writeReportFiles | Source code |
| yield | Source code |
