653 lines
13 KiB
Plaintext
653 lines
13 KiB
Plaintext
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HTSLIB_1.0 {
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bam_aux2A;
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bam_aux2Z;
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bam_aux2f;
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bam_aux2i;
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bam_aux_append;
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bam_aux_del;
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bam_aux_get;
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bam_cigar2qlen;
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bam_cigar2rlen;
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bam_copy1;
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bam_destroy1;
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bam_dup1;
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bam_endpos;
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bam_flag2str;
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bam_hdr_read;
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bam_hdr_write;
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bam_init1;
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bam_mplp_auto;
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bam_mplp_destroy;
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bam_mplp_init;
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bam_mplp_init_overlaps;
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bam_mplp_set_maxcnt;
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bam_plp_auto;
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bam_plp_destroy;
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bam_plp_init;
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bam_plp_next;
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bam_plp_push;
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bam_plp_reset;
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bam_plp_set_maxcnt;
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bam_read1;
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bam_str2flag;
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bam_write1;
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bcf_add_filter;
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bcf_calc_ac;
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bcf_clear;
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bcf_destroy;
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bcf_dup;
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bcf_enc_vchar;
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bcf_enc_vfloat;
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bcf_enc_vint;
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bcf_float_missing;
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bcf_float_vector_end;
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bcf_fmt_array;
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bcf_fmt_sized_array;
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bcf_get_fmt;
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bcf_get_format_string;
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bcf_get_format_values;
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bcf_get_info;
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bcf_get_info_values;
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bcf_get_variant_type;
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bcf_get_variant_types;
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bcf_gt_type;
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bcf_has_filter;
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bcf_hdr_add_hrec;
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bcf_hdr_add_sample;
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bcf_hdr_append;
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bcf_hdr_combine;
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bcf_hdr_destroy;
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bcf_hdr_dup;
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bcf_hdr_fmt_text;
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bcf_hdr_get_hrec;
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bcf_hdr_get_version;
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bcf_hdr_id2int;
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bcf_hdr_init;
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bcf_hdr_parse;
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bcf_hdr_parse_line;
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bcf_hdr_printf;
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bcf_hdr_read;
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bcf_hdr_remove;
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bcf_hdr_seqnames;
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bcf_hdr_set;
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bcf_hdr_set_samples;
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bcf_hdr_set_version;
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bcf_hdr_subset;
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bcf_hdr_sync;
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bcf_hdr_write;
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bcf_hrec_add_key;
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bcf_hrec_destroy;
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bcf_hrec_dup;
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bcf_hrec_find_key;
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bcf_hrec_format;
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bcf_hrec_set_val;
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bcf_index_build;
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bcf_init;
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bcf_is_snp;
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bcf_read;
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bcf_readrec;
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bcf_remove_alleles;
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bcf_remove_filter;
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bcf_sr_add_reader;
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bcf_sr_destroy;
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bcf_sr_init;
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bcf_sr_next_line;
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bcf_sr_regions_destroy;
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bcf_sr_regions_flush;
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bcf_sr_regions_init;
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bcf_sr_regions_next;
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bcf_sr_regions_overlap;
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bcf_sr_regions_seek;
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bcf_sr_remove_reader;
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bcf_sr_seek;
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bcf_sr_set_regions;
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bcf_sr_set_samples;
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bcf_sr_set_targets;
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bcf_subset;
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bcf_subset_format;
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bcf_sweep_bwd;
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bcf_sweep_destroy;
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bcf_sweep_fwd;
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bcf_sweep_hdr;
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bcf_sweep_init;
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bcf_translate;
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bcf_trim_alleles;
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bcf_type_shift;
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bcf_unpack;
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bcf_update_alleles;
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bcf_update_alleles_str;
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bcf_update_filter;
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bcf_update_format;
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bcf_update_format_string;
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bcf_update_id;
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bcf_update_info;
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bcf_write;
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bgzf_check_EOF;
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bgzf_close;
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bgzf_dopen;
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bgzf_flush;
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bgzf_flush_try;
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bgzf_getc;
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bgzf_getline;
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bgzf_hopen;
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bgzf_index_build_init;
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bgzf_index_dump;
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bgzf_index_load;
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bgzf_is_bgzf;
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bgzf_mt;
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bgzf_open;
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bgzf_raw_read;
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bgzf_raw_write;
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bgzf_read;
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bgzf_read_block;
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bgzf_seek;
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bgzf_set_cache_size;
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bgzf_useek;
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bgzf_utell;
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bgzf_write;
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cram_close;
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cram_compress_block;
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cram_dopen;
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cram_eof;
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cram_flush;
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cram_free_block;
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cram_free_container;
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cram_new_block;
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cram_new_container;
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cram_open;
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cram_read_block;
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cram_read_container;
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cram_seek;
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cram_set_header;
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cram_set_option;
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cram_set_voption;
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cram_uncompress_block;
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cram_write_block;
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cram_write_container;
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fai_build;
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fai_destroy;
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fai_fetch;
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fai_load;
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faidx_fetch_nseq;
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faidx_fetch_seq;
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faidx_has_seq;
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hclose;
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hclose_abruptly;
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hdopen;
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hfile_destroy;
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hfile_init;
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hfile_oflags;
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hflush;
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hgetc2;
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hopen;
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hpeek;
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hputc2;
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hputs2;
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hread2;
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hrec_add_idx;
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hseek;
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hts_close;
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hts_file_type;
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hts_get_bgzfp;
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hts_getline;
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hts_idx_destroy;
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hts_idx_finish;
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hts_idx_get_meta;
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hts_idx_get_n_no_coor;
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hts_idx_get_stat;
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hts_idx_init;
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hts_idx_load;
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hts_idx_push;
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hts_idx_save;
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hts_idx_seqnames;
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hts_idx_set_meta;
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hts_itr_destroy;
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hts_itr_next;
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hts_itr_query;
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hts_itr_querys;
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hts_open;
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hts_parse_reg;
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hts_readlines;
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hts_readlist;
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hts_set_fai_filename;
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hts_set_threads;
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hts_verbose;
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hts_version;
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hwrite2;
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kf_betai;
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kf_erfc;
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kf_gammap;
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kf_gammaq;
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kf_lgamma;
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kmemmem;
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knet_close;
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knet_dopen;
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knet_open;
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knet_read;
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knet_seek;
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ksplit_core;
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ksprintf;
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kstrnstr;
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kstrstr;
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kstrtok;
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kt_fisher_exact;
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kvsprintf;
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sam_format1;
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sam_hdr_add_lines;
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sam_hdr_dup;
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sam_hdr_incr_ref;
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sam_hdr_length;
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sam_hdr_parse;
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sam_hdr_read;
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sam_hdr_str;
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sam_hdr_write;
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sam_index_load;
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sam_itr_queryi;
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sam_itr_querys;
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sam_open_mode;
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sam_parse1;
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sam_read1;
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sam_write1;
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seq_nt16_str;
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seq_nt16_table;
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stringify_argv;
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tbx_conf_bed;
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tbx_conf_gff;
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tbx_conf_psltbl;
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tbx_conf_sam;
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tbx_conf_vcf;
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tbx_destroy;
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tbx_index;
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tbx_index_build;
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tbx_index_load;
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tbx_name2id;
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tbx_readrec;
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tbx_seqnames;
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vcf_format;
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vcf_hdr_read;
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vcf_hdr_write;
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vcf_parse;
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vcf_read;
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vcf_write;
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vcf_write_line;
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};
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HTSLIB_1.1 {
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bcf_get_fmt_id;
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bcf_get_info_id;
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faidx_iseq;
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faidx_nseq;
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faidx_seq_len;
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} HTSLIB_1.0;
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HTSLIB_1.2.1 {
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bcf_copy;
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bcf_sr_strerror;
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hisremote;
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hts_detect_format;
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hts_format_description;
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hts_get_format;
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hts_hopen;
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hts_set_opt;
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regidx_destroy;
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regidx_init;
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regidx_insert;
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regidx_nregs;
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regidx_overlap;
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regidx_parse_bed;
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regidx_parse_tab;
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regidx_seq_names;
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regidx_seq_nregs;
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seq_nt16_int;
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} HTSLIB_1.1;
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HTSLIB_1.3 {
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bcf_add_id;
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bcf_empty;
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bcf_hdr_merge;
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bcf_index_build2;
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bcf_index_load2;
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bcf_remove_allele_set;
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bgzf_compress;
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cram_block_append;
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cram_block_get_comp_size;
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cram_block_get_content_id;
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cram_block_get_content_type;
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cram_block_get_crc32;
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cram_block_get_data;
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cram_block_get_offset;
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cram_block_get_uncomp_size;
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cram_block_set_comp_size;
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cram_block_set_content_id;
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cram_block_set_crc32;
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cram_block_set_data;
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cram_block_set_offset;
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cram_block_set_uncomp_size;
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cram_block_size;
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cram_block_update_size;
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cram_container_get_landmarks;
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cram_container_get_length;
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cram_container_get_num_blocks;
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cram_container_is_empty;
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cram_container_set_landmarks;
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cram_container_set_length;
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cram_container_set_num_blocks;
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cram_container_size;
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cram_copy_slice;
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cram_fd_get_fp;
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cram_fd_get_header;
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cram_fd_get_version;
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cram_fd_set_fp;
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cram_fd_set_header;
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cram_fd_set_version;
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cram_major_vers;
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cram_minor_vers;
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cram_store_container;
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cram_transcode_rg;
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hfile_add_scheme_handler;
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hfile_always_local;
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hfile_always_remote;
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hts_format_file_extension;
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hts_idx_load2;
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hts_idx_save_as;
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hts_md5_destroy;
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hts_md5_final;
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hts_md5_hex;
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hts_md5_init;
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hts_md5_reset;
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hts_md5_update;
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hts_open_format;
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hts_opt_add;
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hts_opt_apply;
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hts_opt_free;
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hts_parse_decimal;
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hts_parse_format;
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hts_parse_opt_list;
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int32_put_blk;
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kgetline;
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sam_index_build;
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sam_index_build2;
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sam_index_load2;
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sam_open_mode_opts;
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tbx_index_build2;
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tbx_index_load2;
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} HTSLIB_1.2.1;
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HTSLIB_1.4 {
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bam_auxB2f;
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bam_auxB2i;
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bam_auxB_len;
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bam_aux_update_str;
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bam_mplp_constructor;
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bam_mplp_destructor;
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bam_mplp_reset;
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bam_plp_constructor;
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|
|
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;
|