Class Hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 12]

C__bam_mplp_t
C__bgzidx_t
C__faidx_t
C__hts_idx_t
C__kstring_t
C__linkbuf_t
C_bcf_sr_regions_t
C_bcf_sweep_t
C_regidx_t
C_region_t
Cargs_t
Cari_decoder
Cbam1_core_t
Cbam1_t
Cbam_hdr_t
Cbam_pileup1_t
Cgamgee::BaseQuals	Utility class to handle the memory management of the sam record object for a read base qualities
Cbcf1_t
Cbcf_dec_t
Cbcf_fmt_t
Cbcf_hdr_t
Cbcf_hrec_t
Cbcf_idinfo_t
Cbcf_idpair_t
Cbcf_info_t
Cbcf_sr_t
Cbcf_srs_t
CBGZF
Cbgzf_mtaux_t
Cbgzidx1_t
Cbins_t
Ccache_t
Cgamgee::Cigar	Utility class to manage the memory of the cigar structure
Ccram_beta_decoder
Ccram_block
Ccram_block_compression_hdr
Ccram_block_slice_hdr
Ccram_byte_array_len_decoder
Ccram_byte_array_len_encoder
Ccram_byte_array_stop_decoder
Ccram_codec
Ccram_container
Ccram_decode_job
Ccram_external_decoder
Ccram_fd
Ccram_feature
Ccram_file_def
Ccram_gamma_decoder
Ccram_huffman_code
Ccram_huffman_decoder
Ccram_huffman_encoder
Ccram_index
Ccram_job
Ccram_map
Ccram_metrics
Ccram_range
Ccram_record
Ccram_slice
Ccram_stats
Ccram_subexp_decoder
Ccstate_t
Cfaidx1_t
Cgamgee::Fastq	Utility class to hold one FastA or FastQ record
Cgamgee::FastqIterator	Utility class to enable for-each style iteration in the FastqReader class
Cgamgee::FastqReader	Utility class to read many Fastq records from a stream (e.g. Fastq file, stdin, ...) in a for-each loop in a for-each loop
Cfmt_aux_t
Cgamgee::Genotype	Encodes a genotype
ChFILE
ChFILE_backend
ChFILE_fd
ChFILE_mem
ChFILE_net
Chgacc_t
Chts_cram_idx_t
Chts_itr_t
Chts_opt
Chts_pair64_t
ChtsFile
Cgamgee::utils::HtsFileDeleter	Functor object to delete an htsFile pointer
ChtsFormat
Cgamgee::utils::HtsIndexDeleter	Functor object to delete an hts file index pointer
Cgamgee::utils::HtsIteratorDeleter	Functor object to delete an hts file iterator pointer
Cgamgee::utils::IFStreamDeleter	Functor object to delete an ifstream
Cgamgee::IndexedSamIterator	Utility class to enable for-each style iteration in the IndexedSamReader class
Cgamgee::IndexedSamReader< ITERATOR >	Utility class to read a BAM/CRAM file with an appropriate Sam iterator from an indexed file in a for-each loop. Intervals are passed in using a vector of string coordinates compatible with Samtools. When iteration begins, the iterations (re-)starts at the beginning of the first interval
Cgamgee::IndexedVariantReader< ITERATOR >	Utility class to read an indexed BCF file by intervals using an appropriate Variant iterator in a for-each loop
Cgamgee::IndividualField< TYPE >	A class template to hold the values of a specific Variant's format field for all samples
Cgamgee::IndividualFieldValue< VALUE_TYPE >	A class template to hold the values a format field for a particular sample
Cgamgee::Interval	Utility class to store an genomic location (Interval)
►Citerator
Cgamgee::IndividualFieldIterator< TYPE >	Iterator for VariantField objects
Cgamgee::IndividualFieldValueIterator< VALUE_TYPE >	Iterator for FormatFieldGenericValue objects
Cgamgee::SharedFieldIterator< VALUE_TYPE >	Iterator for SharedField objects
Cgamgee::VariantFiltersIterator	Simple random-access iterator class for VariantFilters objects
CknetFile_s
Cks_isort_stack_t
Cks_tokaux_t
CMD5_CTX
Cmempool_t
►Cgamgee::utils::MergedVCFLUTBase< inputs_2_merged_LUT_is_input_ordered, merged_2_inputs_LUT_is_input_ordered >	Base class to store look up information between fields of merged header and input headers
Cgamgee::utils::MergedVCFAllelesIdxLUT< inputs_2_merged_LUT_is_input_ordered, merged_2_inputs_LUT_is_input_ordered >	LUT class for storing mappings between allele vectors in the merged file and input VCF files Since the #alleles per site is expected to be small, this class sets the number of fields to 10. This makes any subsequent re-allocations unlikely. The function resize_luts_if_needed() will almost always return immediately after failing the if condition
Cgamgee::utils::MergedVCFLUTBase< fields_forward_LUT_ordering, fields_reverse_LUT_ordering >
Cgamgee::utils::MergedVCFLUTBase< samples_forward_LUT_ordering, samples_reverse_LUT_ordering >
Cgamgee::utils::MergedVCFLUTBase< true, true >
CmFILE
►Cgamgee::MultipleVariantIterator	Utility class to enable for-each style iteration in the MultipleVariantReader class
Cgamgee::ReferenceBlockSplittingVariantIterator	Utility class to handle reference blocks while iterating over multiple variant files
Cgamgee::MultipleVariantReader< ITERATOR >	Utility class to read multiple VCF/BCF files with an appropriate iterator in a for-each loop
Cpmap_t
Cpool_alloc_t
Cpool_t
CRansDecSymbol
CRansEncSymbol
Cgamgee::ReadBases	Utility class to handle the memory management of the sam record object for read bases
Cgamgee::ReadGroup	Helper struct to hold one read group record from a sam file header
Cref_entry
Cgamgee::ReferenceIterator	Utility class to access reference bases in a FastA-formatted reference genome
Crefs_t
Creg_t
Cregion1_t
Cregitr_t
Creglist_t
►Cruntime_error
Cgamgee::ChromosomeNotFoundException	Exception class for the case where a chromosome is not found in the reference
Cgamgee::ChromosomeSizeException	Exception class for the case where a chromosome is not found in the reference
Cgamgee::FileOpenException	Exception for the case where there is an error opening a file for reading/writing
Cgamgee::HeaderCompatibilityException	Exception for the case where multiple headers are incompatible in some way
Cgamgee::HeaderReadException	Exception for the case where a file header could not be read
Cgamgee::HtslibException	Catchall exception class for htslib errors
Cgamgee::IndexLoadException	Exception for the case where an index file cannot be opened for a particular file (eg., bam/vcf/bcf)
Cgamgee::SingleInputException	Exception class for the case where a single input is required, but more is provided
Cgamgee::Sam	Utility class to manipulate a Sam record
CSAM_hdr
CSAM_hdr_item_s
CSAM_hdr_tag_s
CSAM_PG
CSAM_RG
CSAM_SQ
Cgamgee::utils::SamBodyDeleter	Functor object to delete a bam1_t pointer
Cgamgee::SamBuilder	Class to build Sam objects from existing data or from scratch
Cgamgee::SamBuilderDataField	Class to hold encoded byte arrays for individual data fields (cigar, bases, etc.) during building of a Sam
Cgamgee::SamHeader	Utility class to hold the header of a sam file
Cgamgee::utils::SamHeaderDeleter	Functor object to delete a bam_hdr_t pointer
Cgamgee::SamIterator	Utility class to enable for-each style iteration in the SamReader class
Cgamgee::SamPairIterator	Utility class to enable for-each style iteration by pairs in the SamReader class
Cgamgee::SamReader< ITERATOR >	Utility class to read a SAM/BAM/CRAM file with an appropriate Sam iterator from a stream (e.g. file, stdin, ...) in a for-each loop
Cgamgee::SamTag< TAG_TYPE >	Class to represent a Sam TAG:TYPE:VALUE entry
Cgamgee::SamWriter	Utility class to write out a SAM/BAM/CRAM file to any stream
Cgamgee::SharedBufferSpan	Represents a section (range of bytes) in the shared memory pool VariantBuilderSharedRegion::m_shared_buffer that is currently in use to store encoded field data
Cgamgee::SharedField< TYPE >	A class template to hold the values of a specific Variant's shared field
Cgamgee::utils::ShortValueOptimizedStorage< ELEMENT_TYPE >
Cgamgee::utils::ShortValueOptimizedStorage< ENCODED_TYPE >
Cspare_bams
Cstring_alloc_t
Cstring_t
Cgamgee::utils::SyncedReaderDeleter	Functor object to delete a bcf_srs_t pointer
Cgamgee::SyncedVariantIterator	Utility class to enable for-each style iteration in the SyncedVariantReader class
Cgamgee::SyncedVariantReader< ITERATOR >	Utility class to read multiple VCF.GZ/BCF files with an appropriate iterator in a for-each loop
Ct_pool
Ct_pool_job
Ct_pool_worker_t
Ct_res
Ct_results_queue
Ctbx_conf_t
Ctbx_intv_t
Ctbx_t
►Cunordered_map
Cgamgee::ReferenceMap	Utility class to create a reference object for all reference operations in Foghorn
Cgamgee::Variant	Utility class to manipulate a Variant record
Cvariant_t
Cgamgee::utils::VariantBodyDeleter	Functor object to delete a bcf1_t pointer
Cgamgee::VariantBuilder	VariantBuilder: construct Variant records from scratch (and, coming soon, from existing Variant records)
Cgamgee::VariantBuilderCoreField< FIELD_TYPE >	Internal VariantBuilder class to represent "core" (non-data-region) fields such as the alignment start and the qual
Cgamgee::VariantBuilderCoreField< float >
Cgamgee::VariantBuilderCoreField< int32_t >
Cgamgee::VariantBuilderIndividualField< ENCODED_TYPE, BULK_CHANGE_TYPE >	Helper class for VariantBuilder to manage the storage and encoding of a single multi-sample individual field
Cgamgee::VariantBuilderIndividualRegion	Helper class for VariantBuilder to manage the fields belonging to the individual region of Variant records
Cgamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >	Class that allows you to efficiently prepare multi-sample data for setting individual fields in VariantBuilder
Cgamgee::VariantBuilderSharedRegion	Helper class for VariantBuilder to manage the fields belonging to the shared region of Variant records
Cgamgee::VariantFilters	Class to manipulate filter field objects without making copies
Cgamgee::VariantHeader	Utility class to hold a variant header
Cgamgee::VariantHeaderBuilder	Utility class to build VariantHeader objects from scratch
Cgamgee::utils::VariantHeaderDeleter	Functor object to delete a bcf_hdr_t pointer
Cgamgee::VariantHeaderMerger< fields_forward_LUT_ordering, fields_reverse_LUT_ordering, samples_forward_LUT_ordering, samples_reverse_LUT_ordering >
Cgamgee::VariantHeaderMerger< true, true, true, true >
►Cgamgee::VariantIterator	Utility class to enable for-each style iteration in the VariantReader class
Cgamgee::IndexedVariantIterator
Cgamgee::VariantReader< ITERATOR >	Utility class to read a VCF/BCF file with an appropriate Variant iterator from a stream (e.g. file, stdin, ...) in a for-each loop
Cgamgee::VariantWriter	Utility class to write out a VCF/BCF file to any stream
Cworker_t
Czfp