/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | record.h | 23 Chrpos_T chrlength; member
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H A D | iit_dump.c | 128 unsigned int divlength, chrlength, low, high, lastpos, pos; in print_runlengths() local
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H A D | parserange.c | 373 Univcoord_T *chroffset, Chrpos_T *chrlength, in Parserange_universal() 547 Univcoord_T *chroffset, Chrpos_T *chrlength, in Parserange_universal_iit()
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H A D | path-solve.c | 1038 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in combine_into_qstart_alts() 1102 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in compute_qstart_paths() 1310 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in add_qstart_local() 2031 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in combine_into_qend_alts() 2094 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in compute_qend_paths() 2290 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in add_qend_local() 2446 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in solve_via_segments_genome() 3197 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in compute_qstart_local() 3325 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in compute_qend_local() 3456 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Path_solve_from_diagonals()
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H A D | splicetrie_build.c | 389 Chrpos_T chrlength, chrpos; in Splicetrie_retrieve_via_splicesites() local 809 Chrpos_T chrlength, chrpos; in Splicetrie_retrieve_via_introns() local 1865 Chrpos_T chrlength; in Splicetrie_npartners() local 2872 Chrpos_T chrlength; in build_via_introns_size() local 3138 Chrpos_T chrlength; in Splicetrie_build_via_introns() local
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H A D | substring.c | 248 Chrpos_T chrlength; member 328 Chrpos_T chrlength; in Substring_alias_circular() local 373 Chrpos_T chrlength; in Substring_unalias_circular() local 1624 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Substring_compute_nmatches() 1827 …_T query_compress, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Substring_new() 2579 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Substring_new_alts_D() 2698 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Substring_new_alts_A() 3907 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) { in Substring_new_donor() 3950 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) { in Substring_new_acceptor() 4030 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) { in Substring_new_startfrag() [all …]
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H A D | knownsplicing.c | 251 Chrpos_T chrlength, chrpos; in Knownsplicing_retrieve_via_splicesites() local
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H A D | kmer-search.c | 453 Chrpos_T chrlength; member 495 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Path_new() 1606 Chrpos_T *exonstarts, genomicpos, chrlength; in search_transcriptome_complete() local 2877 Chrpos_T *exonstarts, genomicpos, chrlength; in search_transcriptome_ends() local 5242 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in combine_ends_plus() 5771 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in combine_ends_minus() 6320 Chrpos_T chrlength; in Kmer_search_genome_ends_exact() local 6492 Chrpos_T chrlength; in Kmer_search_genome_ends_approx() local
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H A D | distant-rna.c | 170 Chrpos_T chrlength; in find_spliceends_rna_plus() local 686 Chrpos_T chrlength; in find_spliceends_rna_minus() local
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H A D | terminal.c | 85 Chrpos_T chrlength; in find_terminals() local
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H A D | gmap.c | 1151 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in update_stage3middle_list() 1255 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in update_stage3list() 1465 Chrpos_T chrlength, chrpos; in stage3_from_usersegment() local 1779 Chrpos_T chrlength; in stage3_from_gregions() local 1982 Chrpos_T *chrlength, bool *plusp, int *genestrand, in middle_piece_local_p() 3633 Chrpos_T chrstart, chrend, chrlength; in check_middle_piece_local() local 4071 Chrpos_T chrlength; in apply_stage3() local
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H A D | stage3hr.c | 3522 Chrpos_T chrlength; in Stage3end_new_terminal() local 3720 … int querylength, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Stage3end_new_precomputed() 3969 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Stage3end_nmatches_substrings() 4310 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Stage3end_new_substrings() 4992 Chrpos_T chrlength, Listpool_T listpool, Method_T method, int level) { in Stage3end_new_substitution() 7391 Chrpos_T chrlength = hit->chrlength; in unalias_circular() local 7490 normalize_coord (Univcoord_T orig, int circularalias, Chrpos_T chrlength) { in normalize_coord() 11281 Chrpos_T chrlength = hit->chrlength; in alias_circular() local 15016 Chrpos_T chrlength; in Stage3end_linearize_5() local 15050 Chrpos_T chrlength; in Stage3end_linearize_3() local
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H A D | snpindex.c | 652 Chrpos_T chrlength; in write_offsets() local 856 Chrpos_T chrlength; in compute_positions() local
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H A D | extension-search.c | 1394 Chrpos_T *chrlength, List_T *sense_hits, List_T *antisense_hits, in process_seed() 1600 Chrpos_T chrlength; in extend_seeds() local
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H A D | simplepair.c | 1532 Chrpos_T chrpos, Chrpos_T chrlength, in print_overlap_sam_line() 1735 int absmq_score, int second_absmq, Chrpos_T chrpos, Chrpos_T chrlength, in Simplepair_overlap_print_sam()
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H A D | iit-read-univ.c | 266 Chrpos_T genomiclength, chrstart, chrend, chrlength; in Univ_IIT_altlocp() local 2126 …v_IIT_update_chrnum (int *chrnum, Univcoord_T *chroffset, Univcoord_T chrhigh, Chrpos_T *chrlength, in Univ_IIT_update_chrnum() 2245 Univ_IIT_get_chrnum (Univcoord_T *chroffset, Univcoord_T *chrhigh, Chrpos_T *chrlength, in Univ_IIT_get_chrnum()
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H A D | pair.c | 3800 Pair_circularpos (int *alias, struct T *pairs, int npairs, Chrpos_T chrlength, bool plusp, int quer… in Pair_circularpos() 5066 Pair_alias_circular (struct T *pairs, int npairs, Chrpos_T chrlength) { in Pair_alias_circular() 5083 Pair_unalias_circular (struct T *pairs, int npairs, Chrpos_T chrlength) { in Pair_unalias_circular() 5851 Univ_IIT_T chromosome_iit, Chrpos_T chrpos, Chrpos_T chrlength, in print_sam_line() 6334 int absmq_score, int second_absmq, Chrpos_T chrpos, Chrpos_T chrlength, in Pair_print_sam() 7068 int npairs, bool watsonp, Chrpos_T chrlength) { in count_psl_blocks_pro() 7342 Chrpos_T chrlength; in Pair_print_pslformat_pro() local 9540 Chrpos_T chrlength, int wraplength, bool include_utr_p) { in Pair_print_mask_introns() 10487 Chrpos_T chrlength, Pairpool_T pairpool, bool plusp) { in Pair_split_circular()
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H A D | stage3hrdef.h | 84 Chrpos_T chrlength; member
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H A D | get-genome.c | 918 Chrpos_T genomiclength, chrlength, chrstart, chrend; in main() local
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H A D | gmapindex.c | 681 Chrpos_T chrlength, alt_scaffold_start, alt_scaffold_end; in write_chromosome_file() local
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H A D | segment-search.c | 508 Chrpos_T chrlength; in make_records() local
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H A D | gregion.c | 72 Chrpos_T chrlength; member
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H A D | genome.c | 10575 Chrpos_T chrlength; in fill_buffer() local
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H A D | stage3.c | 458 Chrpos_T chrlength; member 506 Chrpos_T chrlength, bool watsonp, int genestrand, in Stage3middle_new() 569 Chrpos_T chrlength; member 5902 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Stage3_new() 6048 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) { in Stage3_new_from_pairs() 15690 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Stage3_compute_middle()
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