/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | concordance.c | 437 Listpool_T listpool, Hitlistpool_T hitlistpool) { in do_genome_plus() 568 Listpool_T listpool, Hitlistpool_T hitlistpool) { in do_genome_minus() 707 Listpool_T listpool, Hitlistpool_T hitlistpool, in Concordance_pair_up_genome() 976 Listpool_T listpool, Hitlistpool_T hitlistpool) { in do_distant_plus_plus() 1126 Listpool_T listpool, Hitlistpool_T hitlistpool) { in do_distant_minus_minus() 1275 Listpool_T listpool, Hitlistpool_T hitlistpool) { in do_distant_plus_minus() 1395 Listpool_T listpool, Hitlistpool_T hitlistpool) { in do_distant_minus_plus() 1523 Listpool_T listpool, Hitlistpool_T hitlistpool, in Concordance_pair_up_distant()
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H A D | terminal.c | 64 Compress_T query_compress, Listpool_T listpool, in find_terminals() 284 int genestrand, Listpool_T listpool, in Terminal_solve_plus() 399 int genestrand, Listpool_T listpool, in Terminal_solve_minus()
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H A D | path-solve.c | 182 Listpool_T listpool) { in Path_copy_5() 211 Listpool_T listpool) { in Path_copy_3() 484 Listpool_T listpool, int sensedir) { in attach_qstart_diagonal() 1106 Listpool_T listpool, Univdiagpool_T univdiagpool, int sensedir, bool innerp) { in compute_qstart_paths() 1315 Listpool_T listpool, int sensedir, bool innerp) { in add_qstart_local() 1462 Listpool_T listpool, int sensedir) { in attach_qend_diagonal() 2098 Listpool_T listpool, Univdiagpool_T univdiagpool, int sensedir, bool innerp) { in compute_qend_paths() 2295 Listpool_T listpool, int sensedir, bool innerp) { in add_qend_local() 2449 Listpool_T listpool, Hitlistpool_T hitlistpool, Method_T method, int level) { in solve_via_segments_genome() 3326 Intlistpool_T intlistpool, Univcoordlistpool_T univcoordlistpool, Listpool_T listpool, in compute_qend_local() [all …]
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H A D | distant-rna.c | 143 Compress_T query_compress, Listpool_T listpool, in find_spliceends_rna_plus() 659 Compress_T query_compress, Listpool_T listpool, in find_spliceends_rna_minus() 1202 Listpool_T listpool, Hitlistpool_T hitlistpool, int level) { in find_splicepairs_rna() 1944 int genestrand, bool first_read_p, Listpool_T listpool, in Distant_rna_solve()
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H A D | extension-search.c | 891 int nmismatches_allowed, int genestrand, Listpool_T listpool) { in get_elt_sets_queryfwd() 1146 int nmismatches_allowed, int genestrand, Listpool_T listpool) { in get_elt_sets_queryrev() 1401 Listpool_T listpool, Univdiagpool_T univdiagpool, Hitlistpool_T hitlistpool, in process_seed() 1594 Listpool_T listpool, Univdiagpool_T univdiagpool, Hitlistpool_T hitlistpool, in extend_seeds() 1704 Intlistpool_T intlistpool, Univcoordlistpool_T univcoordlistpool, Listpool_T listpool, in Extension_search()
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H A D | stage1hr.c | 1059 Listpool_T listpool, Univdiagpool_T univdiagpool, Hitlistpool_T hitlistpool, in single_read_search() 1428 Listpool_T listpool, Univdiagpool_T univdiagpool, Hitlistpool_T hitlistpool) { in Stage1_single_read() 1649 Listpool_T listpool, Univdiagpool_T univdiagpool, Hitlistpool_T hitlistpool) { in paired_read_segment_search() 2236 Listpool_T listpool, Univdiagpool_T univdiagpool, Hitlistpool_T hitlistpool) { in paired_read() 2407 Listpool_T listpool, Hitlistpool_T hitlistpool) { in consolidate_paired_results() 2785 Listpool_T listpool, Univdiagpool_T univdiagpool, Hitlistpool_T hitlistpool) { in Stage1_paired_read()
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H A D | distant-dna.c | 83 Listpool_T listpool, Hitlistpool_T hitlistpool, int level) { in Distant_dna_solve()
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H A D | kmer-search.c | 1157 Listpool_T listpool, Hitlistpool_T hitlistpool, int level) { in single_hits_gplus() 1299 Listpool_T listpool, Hitlistpool_T hitlistpool, int level) { in single_hits_gminus() 4607 Listpool_T listpool, Hitlistpool_T hitlistpool, int level) { in Kmer_search_transcriptome_single() 5245 Listpool_T listpool, Hitlistpool_T hitlistpool, int level) { in combine_ends_plus() 5774 Listpool_T listpool, Hitlistpool_T hitlistpool, int level) { in combine_ends_minus() 6310 Listpool_T listpool, Hitlistpool_T hitlistpool, int level) { in Kmer_search_genome_ends_exact() 6468 Listpool_T listpool, Hitlistpool_T hitlistpool, int level) { in Kmer_search_genome_ends_approx()
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H A D | junction.c | 276 Junction_copy_list (List_T old, Listpool_T listpool) { in Junction_copy_list()
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H A D | gsnap.c | 934 Listpool_T listpool, Univdiagpool_T univdiagpool, Hitlistpool_T hitlistpool, in process_request() 1135 Listpool_T listpool; in single_thread() local 1326 Listpool_T listpool; in worker_thread() local
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H A D | segment-search.c | 1107 Listpool_T listpool, Univdiagpool_T univdiagpool, Hitlistpool_T hitlistpool, in solve_all() 1356 Listpool_T listpool, Univdiagpool_T univdiagpool, Hitlistpool_T hitlistpool, in Segment_search_all()
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H A D | stage3hr.c | 3336 Stage3end_copy (T old, Listpool_T listpool) { in Stage3end_copy() 3515 bool gplusp, int genestrand, int sensedir, Listpool_T listpool, in Stage3end_new_terminal() 3721 bool gplusp, int genestrand, int sensedir, Listpool_T listpool, Method_T method, int level) { in Stage3end_new_precomputed() 3970 bool splice5p_in, bool splice3p_in, Listpool_T listpool) { in Stage3end_nmatches_substrings() 4313 Listpool_T listpool, Method_T method, int level) { in Stage3end_new_substrings() 4992 Chrpos_T chrlength, Listpool_T listpool, Method_T method, int level) { in Stage3end_new_substitution() 5277 Listpool_T listpool, Method_T method, int level) { in Stage3end_new_splice() 5612 bool first_read_p, Listpool_T listpool, int level) { in Stage3end_new_distant() 11311 Listpool_T listpool, bool expect_concordant_p, bool transcriptome_guided_p) { in Stage3pair_new()
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H A D | substring.c | 4255 Substring_sort_siteD_halves (List_T hitlist, Listpool_T listpool, bool ascendingp) { in Substring_sort_siteD_halves() 4308 Substring_sort_siteA_halves (List_T hitlist, Listpool_T listpool, bool ascendingp) { in Substring_sort_siteA_halves() 4361 Substring_sort_siteN_halves (List_T hitlist, Listpool_T listpool, bool ascendingp) { in Substring_sort_siteN_halves()
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/dports/security/snort/snort-2.9.18/src/ |
H A D | sf_sdlist.c | 403 SDListItem listpool[1000]; in main() local
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