Here is a list of all file members with links to the files they belong to:

- c -

• category_maximum : hts.h
• check() : fieldarith.c
• check_bam_aux_get() : sam.c
• check_offset() : hfile.c
• cigar_op : cram_samtools.h
• COLLAPSE_ANY : synced_bcf_reader.h
• COLLAPSE_BOTH : synced_bcf_reader.h
• COLLAPSE_INDELS : synced_bcf_reader.h
• COLLAPSE_NONE : synced_bcf_reader.h
• COLLAPSE_SNPS : synced_bcf_reader.h
• COLLAPSE_SOME : synced_bcf_reader.h
• COMPILER_ID : CMakeCCompilerId.c , CMakeCXXCompilerId.cpp
• COMPRESSION_HEADER : cram_structs.h
• compression_maximum : hts.h
• CORE : cram_structs.h
• crai : hts.h
• cram : hts.h
• CRAM_ALL : cram_structs.h
• CRAM_AP : cram_structs.h
• cram_aux : cram_structs.h
• CRAM_aux : cram_structs.h
• CRAM_BA : cram_structs.h
• CRAM_BB : cram_structs.h
• CRAM_BB_len : cram_structs.h
• cram_beta_decode_char() : cram_codecs.c
• cram_beta_decode_free() : cram_codecs.c
• cram_beta_decode_init() : cram_codecs.c
• cram_beta_decode_int() : cram_codecs.c
• cram_beta_encode_char() : cram_codecs.c
• cram_beta_encode_free() : cram_codecs.c
• cram_beta_encode_init() : cram_codecs.c
• cram_beta_encode_int() : cram_codecs.c
• cram_beta_encode_store() : cram_codecs.c
• CRAM_BF : cram_structs.h
• cram_block_method : cram_structs.h
• cram_block_method2str() : cram_io.c , cram_io.h
• CRAM_BS : cram_structs.h
• cram_byte_array_len_decode() : cram_codecs.c
• cram_byte_array_len_decode_free() : cram_codecs.c
• cram_byte_array_len_decode_init() : cram_codecs.c
• cram_byte_array_len_encode() : cram_codecs.c
• cram_byte_array_len_encode_free() : cram_codecs.c
• cram_byte_array_len_encode_init() : cram_codecs.c
• cram_byte_array_len_encode_store() : cram_codecs.c
• cram_byte_array_stop_decode_block() : cram_codecs.c
• cram_byte_array_stop_decode_free() : cram_codecs.c
• cram_byte_array_stop_decode_init() : cram_codecs.c
• cram_byte_array_stop_encode() : cram_codecs.c
• cram_byte_array_stop_encode_free() : cram_codecs.c
• cram_byte_array_stop_encode_init() : cram_codecs.c
• cram_byte_array_stop_encode_store() : cram_codecs.c
• CRAM_CF : cram_structs.h
• cram_cigar : cram_structs.h
• CRAM_CIGAR : cram_structs.h
• cram_close() : cram_io.c , cram_io.h
• cram_codec : cram_codecs.h
• cram_codec_to_id() : cram_codecs.c , cram_codecs.h
• cram_compress_block() : cram_io.c , cram_io.h
• cram_content_type : cram_structs.h
• cram_content_type2str() : cram_io.c , cram_io.h
• cram_decode_compression_header() : cram_decode.c , cram_decode.h
• cram_decode_slice() : cram_decode.c , cram_decode.h
• cram_decode_slice_header() : cram_decode.c , cram_decode.h
• cram_decode_slice_mt() : cram_decode.c
• cram_decode_slice_thread() : cram_decode.c
• cram_decode_TD() : cram_decode.c
• cram_decoder_init() : cram_codecs.c , cram_codecs.h
• cram_dependent_data_series() : cram_decode.c
• CRAM_DL : cram_structs.h
• cram_dopen() : cram_io.c , cram_io.h
• cram_DS_ID : cram_structs.h
• cram_encode_compression_header() : cram_encode.c , cram_encode.h
• cram_encode_container() : cram_encode.c , cram_encode.h
• cram_encode_slice_header() : cram_encode.c , cram_encode.h
• cram_encoder_init() : cram_codecs.c , cram_codecs.h
• cram_encoding : cram_structs.h
• cram_encoding2str() : cram_codecs.c , cram_codecs.h
• cram_eof() : cram_io.c , cram_io.h
• cram_external_decode_char() : cram_codecs.c
• cram_external_decode_free() : cram_codecs.c
• cram_external_decode_init() : cram_codecs.c
• cram_external_decode_int() : cram_codecs.c
• cram_external_encode_char() : cram_codecs.c
• cram_external_encode_free() : cram_codecs.c
• cram_external_encode_init() : cram_codecs.c
• cram_external_encode_int() : cram_codecs.c
• cram_external_encode_store() : cram_codecs.c
• cram_external_type : cram_structs.h
• CRAM_FC : cram_structs.h
• cram_fd : cram_structs.h
• CRAM_FDUP : cram_structs.h
• cram_fields : cram_structs.h
• CRAM_FLAG_DETACHED : cram_structs.h
• CRAM_FLAG_MATE_DOWNSTREAM : cram_structs.h
• CRAM_FLAG_PRESERVE_QUAL_SCORES : cram_structs.h
• cram_flush() : cram_io.c , cram_io.h
• cram_flush_container() : cram_io.c , cram_io.h
• cram_flush_container_mt() : cram_io.c , cram_io.h
• cram_flush_thread() : cram_io.c
• CRAM_FN : cram_structs.h
• CRAM_FP : cram_structs.h
• CRAM_FPAIRED : cram_structs.h
• CRAM_FPROPER_PAIR : cram_structs.h
• CRAM_FQCFAIL : cram_structs.h
• CRAM_FREAD1 : cram_structs.h
• CRAM_FREAD2 : cram_structs.h
• cram_free_block() : cram_io.h , cram_io.c
• cram_free_compression_header() : cram_io.c , cram_io.h
• cram_free_container() : cram_io.c , cram_io.h
• cram_free_file_def() : cram_io.c , cram_io.h
• cram_free_slice() : cram_io.c , cram_io.h
• cram_free_slice_header() : cram_io.c , cram_io.h
• CRAM_FREVERSE : cram_structs.h
• CRAM_FSECONDARY : cram_structs.h
• CRAM_FUNMAP : cram_structs.h
• cram_gamma_decode() : cram_codecs.c
• cram_gamma_decode_free() : cram_codecs.c
• cram_gamma_decode_init() : cram_codecs.c
• cram_get_bam_seq() : cram_decode.c , cram_decode.h
• cram_get_ref() : cram_io.c , cram_io.h
• cram_get_seq() : cram_decode.c , cram_decode.h
• CRAM_HC : cram_structs.h
• cram_header_to_bam() : cram_samtools.c , cram_samtools.h
• cram_huffman_decode_char() : cram_codecs.c
• cram_huffman_decode_char0() : cram_codecs.c
• cram_huffman_decode_free() : cram_codecs.c
• cram_huffman_decode_init() : cram_codecs.c
• cram_huffman_decode_int() : cram_codecs.c
• cram_huffman_decode_int0() : cram_codecs.c
• cram_huffman_encode_char() : cram_codecs.c
• cram_huffman_encode_char0() : cram_codecs.c
• cram_huffman_encode_free() : cram_codecs.c
• cram_huffman_encode_init() : cram_codecs.c
• cram_huffman_encode_int() : cram_codecs.c
• cram_huffman_encode_int0() : cram_codecs.c
• cram_huffman_encode_store() : cram_codecs.c
• CRAM_IN : cram_structs.h
• cram_index : cram_structs.h
• cram_index_build() : cram_index.c , cram_index.h
• cram_index_free() : cram_index.c , cram_index.h
• cram_index_load() : cram_index.c , cram_index.h
• cram_index_query() : cram_index.c , cram_index.h
• CRAM_KEY : cram_io.h
• cram_load_reference() : cram_io.c , cram_io.h
• CRAM_M_REVERSE : cram_structs.h
• CRAM_M_UNMAP : cram_structs.h
• CRAM_MAJOR_VERS : cram_structs.h
• CRAM_MAP : cram_structs.h
• cram_map : cram_structs.h
• CRAM_MAP_HASH : cram_structs.h
• CRAM_MF : cram_structs.h
• CRAM_MINOR_VERS : cram_structs.h
• CRAM_MQ : cram_structs.h
• cram_mstrand : cram_structs.h
• cram_name_len : cram_structs.h
• cram_new_block() : cram_io.h , cram_io.c
• cram_new_compression_header() : cram_io.c , cram_io.h
• cram_new_container() : cram_io.c , cram_io.h
• cram_new_metrics() : cram_io.c , cram_io.h
• cram_new_slice() : cram_io.h , cram_io.c
• CRAM_NF : cram_structs.h
• CRAM_NP : cram_structs.h
• CRAM_NS : cram_structs.h
• cram_open() : cram_io.h , cram_io.c
• CRAM_OPT_DECODE_MD : hts.h
• CRAM_OPT_EMBED_REF : hts.h
• CRAM_OPT_IGNORE_MD5 : hts.h
• CRAM_OPT_MULTI_SEQ_PER_SLICE : hts.h
• CRAM_OPT_NO_REF : hts.h
• CRAM_OPT_NTHREADS : hts.h
• CRAM_OPT_PREFIX : hts.h
• CRAM_OPT_RANGE : hts.h
• CRAM_OPT_REFERENCE : hts.h
• CRAM_OPT_REQUIRED_FIELDS : hts.h
• CRAM_OPT_SEQS_PER_SLICE : hts.h
• CRAM_OPT_SHARED_REF : hts.h
• CRAM_OPT_SLICES_PER_CONTAINER : hts.h
• CRAM_OPT_THREAD_POOL : hts.h
• CRAM_OPT_USE_BZIP2 : hts.h
• CRAM_OPT_USE_LZMA : hts.h
• CRAM_OPT_USE_RANS : hts.h
• CRAM_OPT_VERBOSITY : hts.h
• CRAM_OPT_VERSION : hts.h
• cram_option : hts.h
• CRAM_PD : cram_structs.h
• cram_put_bam_seq() : cram_encode.c , cram_encode.h
• cram_qname : cram_structs.h
• CRAM_QQ : cram_structs.h
• CRAM_QQ_len : cram_structs.h
• CRAM_QS : cram_structs.h
• cram_qual : cram_structs.h
• cram_read_block() : cram_io.h , cram_io.c
• cram_read_container() : cram_io.h , cram_io.c
• cram_read_file_def() : cram_io.h , cram_io.c
• cram_read_SAM_hdr() : cram_io.c , cram_io.h
• cram_read_slice() : cram_io.c , cram_io.h
• cram_ref_decr() : cram_io.c , cram_io.h
• cram_ref_incr() : cram_io.h , cram_io.c
• cram_ref_load() : cram_io.c
• CRAM_RG : cram_structs.h
• CRAM_RI : cram_structs.h
• CRAM_RL : cram_structs.h
• CRAM_RN : cram_structs.h
• CRAM_RS : cram_structs.h
• CRAM_SC : cram_structs.h
• cram_seek() : cram_io.h , cram_io.c
• cram_seek_to_refpos() : cram_index.c , cram_index.h
• CRAM_SEQ : cram_structs.h
• cram_seq : cram_structs.h
• cram_seqi : cram_structs.h
• cram_set_header() : cram_io.h , cram_io.c
• cram_set_option() : cram_io.c , cram_io.h
• cram_set_voption() : cram_io.h , cram_io.c
• cram_slice : cram_structs.h
• cram_stats_add() : cram_stats.h , cram_stats.c
• cram_stats_create() : cram_stats.c , cram_stats.h
• cram_stats_del() : cram_stats.h , cram_stats.c
• cram_stats_dump() : cram_stats.c , cram_stats.h
• cram_stats_encoding() : cram_stats.c , cram_stats.h
• cram_stats_free() : cram_stats.c , cram_stats.h
• cram_strand : cram_structs.h
• cram_subexp_decode() : cram_codecs.c
• cram_subexp_decode_free() : cram_codecs.c
• cram_subexp_decode_init() : cram_codecs.c
• CRAM_SUBST_MATRIX : cram_structs.h
• CRAM_TL : cram_structs.h
• CRAM_TS : cram_structs.h
• cram_uncompress_block() : cram_io.h , cram_io.c
• cram_write_block() : cram_io.h , cram_io.c
• cram_write_container() : cram_io.h , cram_io.c
• cram_write_file_def() : cram_io.h , cram_io.c
• cram_write_SAM_hdr() : cram_io.h , cram_io.c
• csi : hts.h
• CT_ERROR : cram_structs.h
• custom : hts.h
• custom_free() : test-regidx.c
• custom_parse() : test-regidx.c