Index A | C | D | G | I | M | O | P | R | S | U A adjustFeatureBounds() (in module consenrich.core) C cbedMask() (in module consenrich.cconsenrich) cgetFragmentLength() (in module consenrich.cconsenrich) cinvertMatrixE() (in module consenrich.cconsenrich) constructMatrixF() (in module consenrich.core) constructMatrixH() (in module consenrich.core) constructMatrixQ() (in module consenrich.core) countingParams (class in consenrich.core) creadBamSegment() (in module consenrich.cconsenrich) csampleBlockStats() (in module consenrich.cconsenrich) cSparseAvg() (in module consenrich.cconsenrich) D detrendParams (class in consenrich.core) detrendTrack() (in module consenrich.detrorm) G genomeParams (class in consenrich.core) getAverageLocalVarianceTrack() (in module consenrich.core) getBedMask() (in module consenrich.core) getChromRanges() (in module consenrich.core) getChromRangesJoint() (in module consenrich.core) getEffectiveGenomeSize() (in module consenrich.constants) getGenomeResourceFile() (in module consenrich.constants) getMuncTrack() (in module consenrich.core) getPairScaleFactors() (in module consenrich.detrorm) getPrecisionWeightedResidual() (in module consenrich.core) getPrimaryState() (in module consenrich.core) getReadLength() (in module consenrich.core) getScaleFactor1x() (in module consenrich.detrorm) getScaleFactorPerMillion() (in module consenrich.detrorm) getSparseMap() (in module consenrich.core) getStateCovarTrace() (in module consenrich.core) I inputParams (class in consenrich.core) M matchingParams (class in consenrich.core) matchWavelet() (in module consenrich.matching) mergeMatches() (in module consenrich.matching) O observationParams (class in consenrich.core) P processParams (class in consenrich.core) R readBamSegments() (in module consenrich.core) resolveGenomeName() (in module consenrich.constants) runConsenrich() (in module consenrich.core) S samParams (class in consenrich.core) sparseIntersection() (in module consenrich.core) stateParams (class in consenrich.core) U updateProcessNoiseCovariance() (in module consenrich.cconsenrich)