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

- c -

• cache_test() : cache_test.cpp , nvbio-test.cpp
• charf : zconf.h
• CHECK : inflate.h
• check_forward_stream() : packedstream_test.cpp
• check_match : deflate.c
• check_stream() : packedstream_test.cpp
• CHECK_VALUE : crc.h
• cigar_op : cram_samtools.h
• CLEAR_HASH : deflate.c
• Code : deflate.h
• CODELENS : inflate.h
• CODES : inftrees.h
• codetype : inftrees.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
• COMMENT : inflate.h
• COMMENT_STATE : deflate.h
• compress() : compress.c
• compress2() : compress.c
• compress_block() : trees.c
• compressBound() : compress.c
• compressFunc_t : lz4frame.c
• COMPRESSION_HEADER : cram_structs.h
• COMPRESSION_SORTING : blockwise_sufsort.h
• compute_bloom_filter_stats() : bloom_filters.h
• config : deflate.c
• configuration_table : deflate.c
• const : zconf.h
• contentChecksum_t : lz4frame.h
• contentChecksumEnabled : lz4frame.h
• COPY : gzguts.h , inflate.h
• COPY_ : inflate.h
• copy_block() : trees.c
• COPYLENGTH : lz4.c
• CORE : cram_structs.h
• CORRECTIONS : utils.h
• cpu_ksw_test() : cpu.cpp
• cpu_test() : cpu.cpp
• CRAM_1_VERS : cram_structs.h
• CRAM_2_VERS : cram_structs.h
• cram_aux : 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_block_method : cram_structs.h
• cram_block_method2str() : cram_io.c , cram_io.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_char() : 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_cigar : cram_structs.h
• cram_close() : cram_io.c , cram_io.h
• cram_codec : 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_dopen() : cram_io.c , cram_io.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_EXT_BA : cram_structs.h
• CRAM_EXT_IN : cram_structs.h
• CRAM_EXT_NAME : cram_structs.h
• CRAM_EXT_QUAL : cram_structs.h
• CRAM_EXT_REF : cram_structs.h
• CRAM_EXT_SC : cram_structs.h
• CRAM_EXT_TAG : cram_structs.h
• CRAM_EXT_TAG_S : cram_structs.h
• CRAM_EXT_TN : cram_structs.h
• CRAM_EXT_TS_NP : cram_structs.h
• cram_external_decode_block() : cram_codecs.c
• 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() : cram_codecs.c
• cram_external_encode_free() : cram_codecs.c
• cram_external_encode_init() : cram_codecs.c
• cram_external_encode_store() : cram_codecs.c
• cram_external_type : cram_structs.h
• cram_fd : cram_structs.h
• CRAM_FDUP : cram_structs.h
• cram_FILE : 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_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.c , cram_io.h
• 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.h , cram_decode.c
• cram_get_ref() : cram_io.c , cram_io.h
• cram_get_seq() : cram_decode.h , cram_decode.c
• 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_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_map : cram_structs.h
• CRAM_MAP : cram_structs.h
• CRAM_MAP_HASH : cram_structs.h
• cram_mstrand : cram_structs.h
• cram_name_len : cram_structs.h
• cram_new_block() : cram_io.c , cram_io.h
• 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_open() : cram_io.c , cram_io.h
• CRAM_OPT_DECODE_MD : cram_structs.h
• CRAM_OPT_EMBED_REF : cram_structs.h
• CRAM_OPT_IGNORE_MD5 : cram_structs.h
• CRAM_OPT_MULTI_SEQ_PER_SLICE : cram_structs.h
• CRAM_OPT_NO_REF : cram_structs.h
• CRAM_OPT_NTHREADS : cram_structs.h
• CRAM_OPT_PREFIX : cram_structs.h
• CRAM_OPT_RANGE : cram_structs.h
• CRAM_OPT_REFERENCE : cram_structs.h
• CRAM_OPT_SEQS_PER_SLICE : cram_structs.h
• CRAM_OPT_SHARED_REF : cram_structs.h
• CRAM_OPT_SLICES_PER_CONTAINER : cram_structs.h
• CRAM_OPT_THREAD_POOL : cram_structs.h
• CRAM_OPT_USE_BZIP2 : cram_structs.h
• CRAM_OPT_VERBOSITY : cram_structs.h
• CRAM_OPT_VERSION : cram_structs.h
• cram_option : cram_structs.h
• cram_put_bam_seq() : cram_encode.c , cram_encode.h
• cram_qname : cram_structs.h
• cram_qual : cram_structs.h
• cram_read_block() : cram_io.c , cram_io.h
• cram_read_container() : cram_io.c , cram_io.h
• cram_read_file_def() : cram_io.c , cram_io.h
• cram_read_SAM_hdr() : cram_io.c , cram_io.h
• cram_read_slice() : cram_io.c , cram_io.h
• cram_ref_decr() : cram_io.h , cram_io.c
• cram_ref_incr() : cram_io.h , cram_io.c
• cram_ref_load() : cram_io.c
• cram_seek() : cram_io.h , cram_io.c
• cram_seek_to_refpos() : cram_index.c , cram_index.h
• cram_seq : cram_structs.h
• cram_seqi : cram_structs.h
• cram_set_header() : cram_io.c , cram_io.h
• cram_set_option() : cram_io.c , cram_io.h
• cram_set_voption() : cram_io.c , cram_io.h
• cram_slice : cram_structs.h
• cram_stats_add() : cram_stats.h , cram_stats.c
• cram_stats_create() : cram_stats.h , cram_stats.c
• cram_stats_del() : cram_stats.h , cram_stats.c
• cram_stats_dump() : cram_stats.h , cram_stats.c
• cram_stats_encoding() : cram_stats.h , cram_stats.c
• 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_uncompress_block() : cram_io.c , cram_io.h
• cram_write_block() : cram_io.c , cram_io.h
• cram_write_container() : cram_io.c , cram_io.h
• cram_write_file_def() : cram_io.c , cram_io.h
• cram_write_SAM_hdr() : cram_io.c , cram_io.h
• crc : crc.h
• CRC2 : inflate.c
• CRC32 : crc.h
• crc32() : crc32.c
• crc32_combine() : crc32.c
• crc32_combine64() : crc32.c
• crc32_combine_() : crc32.c
• CRC4 : inflate.c
• CRC_FALSE : crc.h
• CRC_NAME : crc.h
• crc_table : crc32.h
• CRC_TRUE : crc.h
• crcCalc() : crc.h
• crcInit() : nvBowtie.cpp , nvbio-test.cpp , crc.cpp , nvbio-aln-diff.cpp , nvSSA.cpp , crc.h
• crcTable : crc.h , crc.cpp
• CSS_KEY_PRUNING : prefix_doubling_sufsort.h
• ct_data : deflate.h
• CT_ERROR : cram_structs.h