| ►Ngamgee | |
| ►Nutils | Utility functions for the gamgee library |
| CHtsFileDeleter | Functor object to delete an htsFile pointer |
| CHtsIndexDeleter | Functor object to delete an hts file index pointer |
| CHtsIteratorDeleter | Functor object to delete an hts file iterator pointer |
| CIFStreamDeleter | Functor object to delete an ifstream |
| CMergedVCFAllelesIdxLUT | 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 |
| CMergedVCFLUTBase | Base class to store look up information between fields of merged header and input headers |
| CSamBodyDeleter | Functor object to delete a bam1_t pointer |
| CSamHeaderDeleter | Functor object to delete a bam_hdr_t pointer |
| CShortValueOptimizedStorage | |
| CSyncedReaderDeleter | Functor object to delete a bcf_srs_t pointer |
| CVariantBodyDeleter | Functor object to delete a bcf1_t pointer |
| CVariantHeaderDeleter | Functor object to delete a bcf_hdr_t pointer |
| CBaseQuals | Utility class to handle the memory management of the sam record object for a read base qualities |
| CChromosomeNotFoundException | Exception class for the case where a chromosome is not found in the reference |
| CChromosomeSizeException | Exception class for the case where a chromosome is not found in the reference |
| CCigar | Utility class to manage the memory of the cigar structure |
| CFastq | Utility class to hold one FastA or FastQ record |
| CFastqIterator | Utility class to enable for-each style iteration in the FastqReader class |
| CFastqReader | 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 |
| CFileOpenException | Exception for the case where there is an error opening a file for reading/writing |
| CGenotype | Encodes a genotype |
| CHeaderCompatibilityException | Exception for the case where multiple headers are incompatible in some way |
| CHeaderReadException | Exception for the case where a file header could not be read |
| CHtslibException | Catchall exception class for htslib errors |
| CIndexedSamIterator | Utility class to enable for-each style iteration in the IndexedSamReader class |
| CIndexedSamReader | 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 |
| CIndexedVariantIterator | |
| CIndexedVariantReader | Utility class to read an indexed BCF file by intervals using an appropriate Variant iterator in a for-each loop |
| CIndexLoadException | Exception for the case where an index file cannot be opened for a particular file (eg., bam/vcf/bcf) |
| CIndividualField | A class template to hold the values of a specific Variant's format field for all samples |
| CIndividualFieldIterator | Iterator for VariantField objects |
| CIndividualFieldValue | A class template to hold the values a format field for a particular sample |
| CIndividualFieldValueIterator | Iterator for FormatFieldGenericValue objects |
| CInterval | Utility class to store an genomic location (Interval) |
| CMultipleVariantIterator | Utility class to enable for-each style iteration in the MultipleVariantReader class |
| CMultipleVariantReader | Utility class to read multiple VCF/BCF files with an appropriate iterator in a for-each loop |
| CReadBases | Utility class to handle the memory management of the sam record object for read bases |
| CReadGroup | Helper struct to hold one read group record from a sam file header |
| CReferenceBlockSplittingVariantIterator | Utility class to handle reference blocks while iterating over multiple variant files |
| CReferenceIterator | Utility class to access reference bases in a FastA-formatted reference genome |
| CReferenceMap | Utility class to create a reference object for all reference operations in Foghorn |
| CSam | Utility class to manipulate a Sam record |
| CSamBuilder | Class to build Sam objects from existing data or from scratch |
| CSamBuilderDataField | Class to hold encoded byte arrays for individual data fields (cigar, bases, etc.) during building of a Sam |
| CSamHeader | Utility class to hold the header of a sam file |
| CSamIterator | Utility class to enable for-each style iteration in the SamReader class |
| CSamPairIterator | Utility class to enable for-each style iteration by pairs in the SamReader class |
| CSamReader | 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 |
| CSamTag | Class to represent a Sam TAG:TYPE:VALUE entry |
| CSamWriter | Utility class to write out a SAM/BAM/CRAM file to any stream |
| CSharedBufferSpan | 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 |
| CSharedField | A class template to hold the values of a specific Variant's shared field |
| CSharedFieldIterator | Iterator for SharedField objects |
| CSingleInputException | Exception class for the case where a single input is required, but more is provided |
| CSyncedVariantIterator | Utility class to enable for-each style iteration in the SyncedVariantReader class |
| CSyncedVariantReader | Utility class to read multiple VCF.GZ/BCF files with an appropriate iterator in a for-each loop |
| CVariant | Utility class to manipulate a Variant record |
| CVariantBuilder | VariantBuilder: construct Variant records from scratch (and, coming soon, from existing Variant records) |
| CVariantBuilderCoreField | Internal VariantBuilder class to represent "core" (non-data-region) fields such as the alignment start and the qual |
| CVariantBuilderIndividualField | Helper class for VariantBuilder to manage the storage and encoding of a single multi-sample individual field |
| CVariantBuilderIndividualRegion | Helper class for VariantBuilder to manage the fields belonging to the individual region of Variant records |
| CVariantBuilderMultiSampleVector | Class that allows you to efficiently prepare multi-sample data for setting individual fields in VariantBuilder |
| CVariantBuilderSharedRegion | Helper class for VariantBuilder to manage the fields belonging to the shared region of Variant records |
| CVariantFilters | Class to manipulate filter field objects without making copies |
| CVariantFiltersIterator | Simple random-access iterator class for VariantFilters objects |
| CVariantHeader | Utility class to hold a variant header |
| CVariantHeaderBuilder | Utility class to build VariantHeader objects from scratch |
| CVariantHeaderMerger | |
| CVariantIterator | Utility class to enable for-each style iteration in the VariantReader class |
| CVariantReader | 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 |
| CVariantWriter | Utility class to write out a VCF/BCF file to any stream |
| 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 | |
| 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 | |
| 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 | |
| Cfmt_aux_t | |
| ChFILE | |
| ChFILE_backend | |
| ChFILE_fd | |
| ChFILE_mem | |
| ChFILE_net | |
| Chgacc_t | |
| Chts_cram_idx_t | |
| Chts_itr_t | |
| Chts_opt | |
| Chts_pair64_t | |
| ChtsFile | |
| ChtsFormat | |
| CknetFile_s | |
| Cks_isort_stack_t | |
| Cks_tokaux_t | |
| CMD5_CTX | |
| Cmempool_t | |
| CmFILE | |
| Cpmap_t | |
| Cpool_alloc_t | |
| Cpool_t | |
| CRansDecSymbol | |
| CRansEncSymbol | |
| Cref_entry | |
| Crefs_t | |
| Creg_t | |
| Cregion1_t | |
| Cregitr_t | |
| Creglist_t | |
| CSAM_hdr | |
| CSAM_hdr_item_s | |
| CSAM_hdr_tag_s | |
| CSAM_PG | |
| CSAM_RG | |
| CSAM_SQ | |
| Cspare_bams | |
| Cstring_alloc_t | |
| Cstring_t | |
| Ct_pool | |
| Ct_pool_job | |
| Ct_pool_worker_t | |
| Ct_res | |
| Ct_results_queue | |
| Ctbx_conf_t | |
| Ctbx_intv_t | |
| Ctbx_t | |
| Cvariant_t | |
| Cworker_t | |
| Czfp | |
1.8.8
