Cbpp::SiteFrequencySpectrumMafStatistics::Categorizer | |
▼Cbpp::Clonable [external] | |
▼Cbpp::Range< size_t > [external] | |
Cbpp::SeqRange | Coordinate range on a sequence. Stores coordinates as a Range<size_t> object, but also keep the strand information |
▼Cbpp::CoreSequence [external] | |
►Cbpp::AbstractCoreSequence [external] | |
►Cbpp::SequenceWithAnnotation [external] | |
Cbpp::MafSequence | A sequence class which is used to store data from MAF files |
►Cbpp::CoreSequenceSymbolList< class > [external] | |
►Cbpp::Sequence [external] | |
Cbpp::SequenceWithAnnotation [external] | |
▼Cbpp::CruxSymbolList [external] | |
►Cbpp::CoreSymbolList< class > [external] | |
►CSymbolList< int > [external] | |
►CEdSymbolList< int > [external] | |
►Cbpp::EdIntSymbolList [external] | |
Cbpp::SequenceWithAnnotation [external] | |
Cbpp::CoreSequenceSymbolList< class > [external] | |
►Cbpp::EdCoreSymbolList< class > [external] | |
CEdSymbolList< int > [external] | |
Cbpp::MafBlock | A synteny block data structure, the basic unit of a MAF alignement file |
▼Cbpp::SequenceFeature | The base interface for sequence features |
Cbpp::BasicSequenceFeature | A very simple implementation of the SequenceFeature class |
▼Cbpp::Commentable [external] | |
Cbpp::AbstractCoreSequence [external] | |
▼Cbpp::FeatureReader | Interface for feature readers |
Cbpp::BedGraphFeatureReader | A simple reader for features in the BedGraph format |
Cbpp::GffFeatureReader | A simple reader implementing the Gene Finding Feature format |
Cbpp::GtfFeatureReader | A simple reader implementing the Gene Transfer Format |
▼Cbpp::IOFormat [external] | |
▼Cbpp::IOSequenceStream [external] | |
►Cbpp::ISequenceStream [external] | |
Cbpp::Fastq | The fastq sequence file format |
►Cbpp::OSequenceStream [external] | |
Cbpp::Fastq | The fastq sequence file format |
▼Cbpp::IterationListener | Listener which enables to catch events when parsing a Maf file |
▼Cbpp::AbstractStatisticsOutputIterationListener | Iteration listener that works with a SequenceStatisticsMafIterator, enabling output of results in a file (partial implementation, format-independent) |
Cbpp::CsvStatisticsOutputIterationListener | Iteration listener that works with a SequenceStatisticsMafIterator, enabling output of results in a file in CSv format |
▼Cbpp::MafIterator | Interface to loop over maf alignment blocks |
▼Cbpp::AbstractMafIterator | Partial implementation of the MafIterator interface |
►Cbpp::AbstractFilterMafIterator | Helper class for developping filter for maf blocks |
Cbpp::AlignmentFilter2MafIterator | Filter maf blocks to remove ambiguously aligned or non-informative regions |
Cbpp::AlignmentFilterMafIterator | Filter maf blocks to remove ambiguously aligned or non-informative regions |
Cbpp::BlockLengthMafIterator | Filter maf blocks to keep only the ones with a minimum number of sites |
Cbpp::BlockMergerMafIterator | Merge blocks if some of their sequences are contiguous |
Cbpp::BlockSizeMafIterator | Filter maf blocks to keep only the ones with a minimum number of species |
Cbpp::ChromosomeMafIterator | Filter maf blocks to keep only the block corresponding to one chromosome (of a reference sequence) |
Cbpp::ConcatenateMafIterator | Concatenate blocks up to a certain size |
Cbpp::CoordinateTranslatorMafIterator | Translate features coordinates from one species to another, based on the alignment |
Cbpp::CoordinatesOutputMafIterator | Output each sequence coordinates for each block |
Cbpp::DuplicateFilterMafIterator | Filter maf blocks to remove duplicated blocks, according to a reference sequence) |
Cbpp::EntropyFilterMafIterator | Filter maf blocks highly divergent regions |
Cbpp::FeatureExtractorMafIterator | Extract alignments corresponding to sequence features given as a vector of SequenceFeature objects |
Cbpp::FeatureFilterMafIterator | Remove from alignment all positions that fall within any feature from a list given as a SequenceFeatureSet object |
Cbpp::FullGapFilterMafIterator | Filter maf blocks to remove in each block the positions made only of gaps |
Cbpp::MafIteratorSynchronizer | This special iterator synchronizes two adaptors |
Cbpp::MaskFilterMafIterator | Filter maf blocks to remove regions with masked positions |
Cbpp::MsmcOutputMafIterator | This iterator outputs all SNPs in the format readable by MSMC |
Cbpp::OrderFilterMafIterator | This iterator check that blocks are ordered according to a reference sequence |
Cbpp::OrphanSequenceFilterMafIterator | Filter maf blocks to keep a the ones which display a specified combination of species |
Cbpp::OutputAlignmentMafIterator | This iterator forward the iterator given as input after having printed its content to an alignment file. The syntax for ENSEMBL meta data is used |
Cbpp::OutputMafIterator | This iterator forward the iterator given as input after having printed its content to a file |
Cbpp::PlinkOutputMafIterator | This iterator outputs all biallelic SNPs in the PLINK format (ped and map files) |
Cbpp::QualityFilterMafIterator | Filter maf blocks to remove regions with low quality |
Cbpp::RemoveEmptySequencesMafIterator | Remove ga-only or unresolved and gap-only sequences in each block |
Cbpp::SequenceFilterMafIterator | Filter maf blocks to keep a subset of sequences, given their name. this filter can also be used to filter block which contain a certain set of sequences |
Cbpp::SequenceLDhotOutputMafIterator | This iterator forward the iterator given as input after having printed its content to an alignment file |
Cbpp::SequenceStatisticsMafIterator | Compute a series of sequence statistics for each block |
Cbpp::TableOutputMafIterator | This iterator outputs sequence states for selected species and positions |
Cbpp::VcfOutputMafIterator | This iterator performs a simple SNP call from the MAF blocks, and outputs the results in the Variant Call Format (VCF) |
Cbpp::WindowSplitMafIterator | Splits block into windows of given sizes |
Cbpp::MafParser | MAF file parser |
Cbpp::SequenceStreamToMafIterator | A MafIterator built from a sequence stream |
Cbpp::TrashIteratorAdapter | |
▼Cbpp::MafStatistics | General interface for computing statistics based on a Maf block |
▼Cbpp::AbstractMafStatistics | Partial implementation of MafStatistics, for convenience |
Cbpp::CharacterCountsMafStatistics | Compute the base frequencies of a maf block |
Cbpp::FourSpeciesPatternCountsMafStatistics | Compute the frequency of site patterns for a quadruplet of species |
Cbpp::PolymorphismMafStatistics | Counts number of polymorphic / fixed sites in two populations |
Cbpp::SequenceDiversityMafStatistics | Provide estimates of sequence diversity |
Cbpp::SiteFrequencySpectrumMafStatistics | Compute the Site Frequency Spectrum of a maf block |
Cbpp::SiteMafStatistics | Compute a few site statistics in a maf block |
▼Cbpp::AbstractMafStatisticsSimple | Partial implementation of MafStatistics, for convenience |
Cbpp::AlignmentScoreMafStatistics | Retrieves the alignment score of a maf block |
Cbpp::BlockLengthMafStatistics | Computes the number of columns in a maf block |
Cbpp::BlockSizeMafStatistics | Computes the number of sequences in a maf block |
Cbpp::PairwiseDivergenceMafStatistics | Computes the pairwise divergence for a pair of sequences in a maf block |
Cbpp::SequenceLengthMafStatistics | Retrieve the sequence length (number of nucleotides) for a given species in a maf block |
▼Cbpp::AbstractSpeciesMultipleSelectionMafStatistics | Partial implementation of MafStatistics for method working on multiple distinct subsets of species, in a site-wise manner |
Cbpp::PolymorphismMafStatistics | Counts number of polymorphic / fixed sites in two populations |
▼Cbpp::AbstractSpeciesSelectionMafStatistics | Partial implementation of MafStatistics for method working on a subset of species, in a site-wise manner |
Cbpp::CharacterCountsMafStatistics | Compute the base frequencies of a maf block |
Cbpp::FourSpeciesPatternCountsMafStatistics | Compute the frequency of site patterns for a quadruplet of species |
Cbpp::SequenceDiversityMafStatistics | Provide estimates of sequence diversity |
Cbpp::SiteFrequencySpectrumMafStatistics | Compute the Site Frequency Spectrum of a maf block |
Cbpp::SiteMafStatistics | Compute a few site statistics in a maf block |
▼Cbpp::MafStatisticsResult | General interface for storing statistical results |
Cbpp::SimpleMafStatisticsResult | A simple maf statistics result, with only one value |
▼Cbpp::MafTrashIterator | Interface to loop over removed blocks of a maf alignment |
Cbpp::AlignmentFilter2MafIterator | Filter maf blocks to remove ambiguously aligned or non-informative regions |
Cbpp::AlignmentFilterMafIterator | Filter maf blocks to remove ambiguously aligned or non-informative regions |
Cbpp::EntropyFilterMafIterator | Filter maf blocks highly divergent regions |
Cbpp::FeatureFilterMafIterator | Remove from alignment all positions that fall within any feature from a list given as a SequenceFeatureSet object |
Cbpp::MaskFilterMafIterator | Filter maf blocks to remove regions with masked positions |
Cbpp::QualityFilterMafIterator | Filter maf blocks to remove regions with low quality |
Cbpp::SequenceFeatureSet | A simple ensemble of sequence features |
Cbpp::SequenceFeatureTools | |