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680 lines (656 loc) · 13.2 KB
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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;
HTSLIB_1.22 {
bcf_format_gt_v2;
bcf_sr_add_hreader;
hts_crc32;
hts_tpool_worker_id;
} HTSLIB_1.21;
HTSLIB_1.23 {
sam_hdr_get;
sam_hdr_set;
} HTSLIB_1.22;
HTSLIB_1.24 {
bcf_itr_querys1;
bcf_itr_regarray;
kfgetline;
khgetline;
tbx_itr_next1;
tbx_itr_querys1;
tbx_itr_regarray;
} HTSLIB_1.23;
HTSLIB_1.25 {
bcf_itr_regions;
sam_hdr_remove_tag_all;
tbx_itr_regions;
} HTSLIB_1.24;