htslib.map

HTSLIB_1.0 {
    bam_aux2A;
    bam_aux2Z;
    bam_aux2f;
    bam_aux2i;
    bam_aux_append;
    bam_aux_del;
    bam_aux_get;
    bam_cigar2qlen;
    bam_cigar2rlen;
    bam_copy1;
    bam_destroy1;
    bam_dup1;
    bam_endpos;
    bam_flag2str;
    bam_hdr_read;
    bam_hdr_write;
    bam_init1;
    bam_mplp_auto;
    bam_mplp_destroy;
    bam_mplp_init;
    bam_mplp_init_overlaps;
    bam_mplp_set_maxcnt;
    bam_plp_auto;
    bam_plp_destroy;
    bam_plp_init;
    bam_plp_next;
    bam_plp_push;
    bam_plp_reset;
    bam_plp_set_maxcnt;
    bam_read1;
    bam_str2flag;
    bam_write1;
    bcf_add_filter;
    bcf_calc_ac;
    bcf_clear;
    bcf_destroy;
    bcf_dup;
    bcf_enc_vchar;
    bcf_enc_vfloat;
    bcf_enc_vint;
    bcf_float_missing;
    bcf_float_vector_end;
    bcf_fmt_array;
    bcf_fmt_sized_array;
    bcf_get_fmt;
    bcf_get_format_string;
    bcf_get_format_values;
    bcf_get_info;
    bcf_get_info_values;
    bcf_get_variant_type;
    bcf_get_variant_types;
    bcf_gt_type;
    bcf_has_filter;
    bcf_hdr_add_hrec;
    bcf_hdr_add_sample;
    bcf_hdr_append;
    bcf_hdr_combine;
    bcf_hdr_destroy;
    bcf_hdr_dup;
    bcf_hdr_fmt_text;
    bcf_hdr_get_hrec;
    bcf_hdr_get_version;
    bcf_hdr_id2int;
    bcf_hdr_init;
    bcf_hdr_parse;
    bcf_hdr_parse_line;
    bcf_hdr_printf;
    bcf_hdr_read;
    bcf_hdr_remove;
    bcf_hdr_seqnames;
    bcf_hdr_set;
    bcf_hdr_set_samples;
    bcf_hdr_set_version;
    bcf_hdr_subset;
    bcf_hdr_sync;
    bcf_hdr_write;
    bcf_hrec_add_key;
    bcf_hrec_destroy;
    bcf_hrec_dup;
    bcf_hrec_find_key;
    bcf_hrec_format;
    bcf_hrec_set_val;
    bcf_index_build;
    bcf_init;
    bcf_is_snp;
    bcf_read;
    bcf_readrec;
    bcf_remove_alleles;
    bcf_remove_filter;
    bcf_sr_add_reader;
    bcf_sr_destroy;
    bcf_sr_init;
    bcf_sr_next_line;
    bcf_sr_regions_destroy;
    bcf_sr_regions_flush;
    bcf_sr_regions_init;
    bcf_sr_regions_next;
    bcf_sr_regions_overlap;
    bcf_sr_regions_seek;
    bcf_sr_remove_reader;
    bcf_sr_seek;
    bcf_sr_set_regions;
    bcf_sr_set_samples;
    bcf_sr_set_targets;
    bcf_subset;
    bcf_subset_format;
    bcf_sweep_bwd;
    bcf_sweep_destroy;
    bcf_sweep_fwd;
    bcf_sweep_hdr;
    bcf_sweep_init;
    bcf_translate;
    bcf_trim_alleles;
    bcf_type_shift;
    bcf_unpack;
    bcf_update_alleles;
    bcf_update_alleles_str;
    bcf_update_filter;
    bcf_update_format;
    bcf_update_format_string;
    bcf_update_id;
    bcf_update_info;
    bcf_write;
    bgzf_check_EOF;
    bgzf_close;
    bgzf_dopen;
    bgzf_flush;
    bgzf_flush_try;
    bgzf_getc;
    bgzf_getline;
    bgzf_hopen;
    bgzf_index_build_init;
    bgzf_index_dump;
    bgzf_index_load;
    bgzf_is_bgzf;
    bgzf_mt;
    bgzf_open;
    bgzf_raw_read;
    bgzf_raw_write;
    bgzf_read;
    bgzf_read_block;
    bgzf_seek;
    bgzf_set_cache_size;
    bgzf_useek;
    bgzf_utell;
    bgzf_write;
    cram_close;
    cram_compress_block;
    cram_dopen;
    cram_eof;
    cram_flush;
    cram_free_block;
    cram_free_container;
    cram_new_block;
    cram_new_container;
    cram_open;
    cram_read_block;
    cram_read_container;
    cram_seek;
    cram_set_header;
    cram_set_option;
    cram_set_voption;
    cram_uncompress_block;
    cram_write_block;
    cram_write_container;
    fai_build;
    fai_destroy;
    fai_fetch;
    fai_load;
    faidx_fetch_nseq;
    faidx_fetch_seq;
    faidx_has_seq;
    hclose;
    hclose_abruptly;
    hdopen;
    hfile_destroy;
    hfile_init;
    hfile_oflags;
    hflush;
    hgetc2;
    hopen;
    hpeek;
    hputc2;
    hputs2;
    hread2;
    hrec_add_idx;
    hseek;
    hts_close;
    hts_file_type;
    hts_get_bgzfp;
    hts_getline;
    hts_idx_destroy;
    hts_idx_finish;
    hts_idx_get_meta;
    hts_idx_get_n_no_coor;
    hts_idx_get_stat;
    hts_idx_init;
    hts_idx_load;
    hts_idx_push;
    hts_idx_save;
    hts_idx_seqnames;
    hts_idx_set_meta;
    hts_itr_destroy;
    hts_itr_next;
    hts_itr_query;
    hts_itr_querys;
    hts_open;
    hts_parse_reg;
    hts_readlines;
    hts_readlist;
    hts_set_fai_filename;
    hts_set_threads;
    hts_verbose;
    hts_version;
    hwrite2;
    kf_betai;
    kf_erfc;
    kf_gammap;
    kf_gammaq;
    kf_lgamma;
    kmemmem;
    knet_close;
    knet_dopen;
    knet_open;
    knet_read;
    knet_seek;
    ksplit_core;
    ksprintf;
    kstrnstr;
    kstrstr;
    kstrtok;
    kt_fisher_exact;
    kvsprintf;
    sam_format1;
    sam_hdr_add_lines;
    sam_hdr_dup;
    sam_hdr_incr_ref;
    sam_hdr_length;
    sam_hdr_parse;
    sam_hdr_read;
    sam_hdr_str;
    sam_hdr_write;
    sam_index_load;
    sam_itr_queryi;
    sam_itr_querys;
    sam_open_mode;
    sam_parse1;
    sam_read1;
    sam_write1;
    seq_nt16_str;
    seq_nt16_table;
    stringify_argv;
    tbx_conf_bed;
    tbx_conf_gff;
    tbx_conf_psltbl;
    tbx_conf_sam;
    tbx_conf_vcf;
    tbx_destroy;
    tbx_index;
    tbx_index_build;
    tbx_index_load;
    tbx_name2id;
    tbx_readrec;
    tbx_seqnames;
    vcf_format;
    vcf_hdr_read;
    vcf_hdr_write;
    vcf_parse;
    vcf_read;
    vcf_write;
    vcf_write_line;
};

HTSLIB_1.1 {
    bcf_get_fmt_id;
    bcf_get_info_id;
    faidx_iseq;
    faidx_nseq;
    faidx_seq_len;
} HTSLIB_1.0;


HTSLIB_1.2.1 {
    bcf_copy;
    bcf_sr_strerror;
    hisremote;
    hts_detect_format;
    hts_format_description;
    hts_get_format;
    hts_hopen;
    hts_set_opt;
    regidx_destroy;
    regidx_init;
    regidx_insert;
    regidx_nregs;
    regidx_overlap;
    regidx_parse_bed;
    regidx_parse_tab;
    regidx_seq_names;
    regidx_seq_nregs;
    seq_nt16_int;
} HTSLIB_1.1;

HTSLIB_1.3 {
    bcf_add_id;
    bcf_empty;
    bcf_hdr_merge;
    bcf_index_build2;
    bcf_index_load2;
    bcf_remove_allele_set;
    bgzf_compress;
    cram_block_append;
    cram_block_get_comp_size;
    cram_block_get_content_id;
    cram_block_get_content_type;
    cram_block_get_crc32;
    cram_block_get_data;
    cram_block_get_offset;
    cram_block_get_uncomp_size;
    cram_block_set_comp_size;
    cram_block_set_content_id;
    cram_block_set_crc32;
    cram_block_set_data;
    cram_block_set_offset;
    cram_block_set_uncomp_size;
    cram_block_size;
    cram_block_update_size;
    cram_container_get_landmarks;
    cram_container_get_length;
    cram_container_get_num_blocks;
    cram_container_is_empty;
    cram_container_set_landmarks;
    cram_container_set_length;
    cram_container_set_num_blocks;
    cram_container_size;
    cram_copy_slice;
    cram_fd_get_fp;
    cram_fd_get_header;
    cram_fd_get_version;
    cram_fd_set_fp;
    cram_fd_set_header;
    cram_fd_set_version;
    cram_major_vers;
    cram_minor_vers;
    cram_store_container;
    cram_transcode_rg;
    hfile_add_scheme_handler;
    hfile_always_local;
    hfile_always_remote;
    hts_format_file_extension;
    hts_idx_load2;
    hts_idx_save_as;
    hts_md5_destroy;
    hts_md5_final;
    hts_md5_hex;
    hts_md5_init;
    hts_md5_reset;
    hts_md5_update;
    hts_open_format;
    hts_opt_add;
    hts_opt_apply;
    hts_opt_free;
    hts_parse_decimal;
    hts_parse_format;
    hts_parse_opt_list;
    int32_put_blk;
    kgetline;
    sam_index_build;
    sam_index_build2;
    sam_index_load2;
    sam_open_mode_opts;
    tbx_index_build2;
    tbx_index_load2;
} HTSLIB_1.2.1;

HTSLIB_1.4 {
    bam_auxB2f;
    bam_auxB2i;
    bam_auxB_len;
    bam_aux_update_str;
    bam_mplp_constructor;
    bam_mplp_destructor;
    bam_mplp_reset;
    bam_plp_constructor;
    bam_plp_destructor;
    bcf_hdr_format;
    bcf_index_build3;
    bcf_sr_destroy_threads;
    bcf_sr_set_opt;
    bcf_sr_set_threads;
    bgzf_block_write;
    bgzf_compression;
    bgzf_index_dump_hfile;
    bgzf_index_load_hfile;
    bgzf_thread_pool;
    cram_check_EOF;
    cram_get_refs;
    errmod_cal;
    errmod_destroy;
    errmod_init;
    fai_build3;
    fai_load3;
    hgetdelim;
    hgets;
    hts_check_EOF;
    hts_json_fnext;
    hts_json_fskip_value;
    hts_json_snext;
    hts_json_sskip_value;
    hts_realloc_or_die;
    hts_set_cache_size;
    hts_set_thread_pool;
    hts_tpool_delete_result;
    hts_tpool_destroy;
    hts_tpool_dispatch;
    hts_tpool_dispatch2;
    hts_tpool_init;
    hts_tpool_kill;
    hts_tpool_next_result;
    hts_tpool_next_result_wait;
    hts_tpool_process_attach;
    hts_tpool_process_destroy;
    hts_tpool_process_detach;
    hts_tpool_process_empty;
    hts_tpool_process_flush;
    hts_tpool_process_init;
    hts_tpool_process_len;
    hts_tpool_process_qsize;
    hts_tpool_process_ref_decr;
    hts_tpool_process_ref_incr;
    hts_tpool_process_reset;
    hts_tpool_process_shutdown;
    hts_tpool_process_sz;
    hts_tpool_result_data;
    hts_tpool_size;
    hts_tpool_wake_dispatch;
    kputd;
    probaln_glocal;
    sam_cap_mapq;
    sam_index_build3;
    sam_prob_realn;
    tbx_index_build3;
} HTSLIB_1.3;

HTSLIB_1.5 {
    hfile_set_blksize;
    hts_get_log_level;
    hts_log;
    hts_set_log_level;
} HTSLIB_1.4;

HTSLIB_1.6 {
    hts_drand48;
    hts_erand48;
    hts_lrand48;
    hts_srand48;
} HTSLIB_1.5;

HTSLIB_1.7 {
    hfile_mem_get_buffer;
    hfile_mem_steal_buffer;
    hts_itr_multi_bam;
    hts_itr_multi_cram;
    hts_itr_multi_next;
    hts_itr_regions;
    hts_json_alloc_token;
    hts_json_free_token;
    hts_json_token_str;
    hts_json_token_type;
    hts_reglist_free;
    sam_hdr_change_HD;
    sam_itr_regions;
} HTSLIB_1.6;

HTSLIB_1.9 {
    bam_aux_update_array;
    bam_aux_update_float;
    bam_aux_update_int;
    fai_fetchqual;
    fai_load3_format;
    fai_load_format;
    faidx_fetch_qual;
} HTSLIB_1.7;

HTSLIB_1.10 {
    bam_cigar_table;
    bam_mplp64_auto;
    bam_plp64_auto;
    bam_plp64_next;
    bam_plp_insertion;
    bam_set_qname;
    bcf_idx_init;
    bcf_idx_save;
    bcf_index_load3;
    bgzf_peek;
    fai_fetch64;
    fai_fetchqual64;
    fai_parse_region;
    fai_set_cache_size;
    faidx_fetch_qual64;
    faidx_fetch_seq64;
    haddextension;
    hts_free;
    hts_idx_fmt;
    hts_idx_load3;
    hts_idx_tbi_name;
    hts_parse_reg64;
    hts_parse_region;
    hts_reglist_create;
    hts_resize_array_;
    hts_tpool_dispatch3;
    kgetline2;
    regidx_init_string;
    regidx_insert_list;
    regidx_parse_reg;
    regidx_parse_vcf;
    regidx_push;
    regitr_copy;
    regitr_destroy;
    regitr_init;
    regitr_loop;
    regitr_overlap;
    regitr_reset;
    sam_hdr_add_line;
    sam_hdr_add_pg;
    sam_hdr_count_lines;
    sam_hdr_destroy;
    sam_hdr_find_line_id;
    sam_hdr_find_line_pos;
    sam_hdr_find_tag_id;
    sam_hdr_find_tag_pos;
    sam_hdr_init;
    sam_hdr_line_index;
    sam_hdr_line_name;
    sam_hdr_name2tid;
    sam_hdr_nref;
    sam_hdr_pg_id;
    sam_hdr_remove_except;
    sam_hdr_remove_line_id;
    sam_hdr_remove_line_pos;
    sam_hdr_remove_lines;
    sam_hdr_remove_tag_id;
    sam_hdr_tid2len;
    sam_hdr_tid2name;
    sam_hdr_update_line;
    sam_idx_init;
    sam_idx_save;
    sam_index_load3;
    sam_itr_regarray;
    sam_parse_region;
    tbx_index_load3;
} HTSLIB_1.9;

HTSLIB_1.11 {
    fai_path;
    hts_lib_shutdown;
    hts_tpool_process_is_shutdown;
    vcf_open_mode;
} HTSLIB_1.10;

HTSLIB_1.12 {
    bam_parse_cigar;
    bam_set1;
    hfile_has_plugin;
    hfile_list_plugins;
    hfile_list_schemes;
    hts_feature_string;
    hts_features;
    hts_filter_eval;
    hts_filter_free;
    hts_filter_init;
    hts_set_filter_expression;
    hts_test_feature;
    sam_parse_cigar;
    sam_passes_filter;
} HTSLIB_1.11;

HTSLIB_1.13 {
    hts_idx_nseq;
} HTSLIB_1.12;

HTSLIB_1.14 {
    bam_mods_at_next_pos;
    bam_mods_at_qpos;
    bam_next_basemod;
    bam_parse_basemod;
    bam_plp_insertion_mod;
    hts_base_mod_state_alloc;
    hts_base_mod_state_free;
    hts_flush;
} HTSLIB_1.13;

HTSLIB_1.15 {
    hts_detect_format2;
} HTSLIB_1.14;

HTSLIB_1.16 {
    bam_mods_query_type;
    bam_mods_recorded;
    bcf_has_variant_type;
    bcf_has_variant_types;
    bcf_variant_length;
    cram_decode_slice_header;
    cram_free_slice_header;
    cram_slice_hdr_get_coords;
    cram_slice_hdr_get_embed_ref_id;
    cram_slice_hdr_get_num_blocks;
    hts_filter_eval2;
} HTSLIB_1.15;

HTSLIB_1.17 {
    bam_aux_first;
    bam_aux_next;
    bam_aux_remove;
    bcf_strerror;
    cram_block_get_method;
    cram_cid2ds_free;
    cram_cid2ds_query;
    cram_codec_describe;
    cram_codec_get_content_ids;
    cram_container_get_num_bases;
    cram_container_get_num_records;
    cram_decode_compression_header;
    cram_describe_encodings;
    cram_expand_method;
    cram_free_compression_header;
    cram_update_cid2ds_map;
    fai_adjust_region;
    fai_line_length;
    faidx_seq_len64;
} HTSLIB_1.16;

HTSLIB_1.18 {
    bam_mods_queryi;
    bam_parse_basemod2;
    fai_thread_pool;
} HTSLIB_1.17;

HTSLIB_1.20 {
    tbx_conf_gaf;
} HTSLIB_1.18;

HTSLIB_1.21 {
    cram_container_get_coords;
    cram_container_num2offset;
    cram_container_offset2num;
    cram_filter_container;
    cram_index_extents;
    cram_num_containers;
    cram_num_containers_between;
} HTSLIB_1.20;