| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | chrom.c | 49 bool circularp; member
70 return this->circularp; in Chrom_circularp()
95 bool circularp, Chrpos_T alt_scaffold_start, Chrpos_T alt_scaffold_end) { in Chrom_from_string() argument
104 new->circularp = circularp; in Chrom_from_string()
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| H A D | chrom.h | 24 bool circularp, Chrpos_T alt_scaffold_start, Chrpos_T alt_scaffold_end);
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| H A D | stage3hrdef.h | 246 bool circularp; /* If either hit5 or hit3 are circular */ member
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| H A D | chimera.h | 54 int queryntlength, int chimera_slop, bool *circularp, bool localp);
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| H A D | gmapindex.c | 348 int contigtype, unsigned int universal_coord, bool circularp, in store_accession() argument
356 chrom = Chrom_from_string(chr_string,mitochondrial_string,order,circularp, in store_accession()
359 chrom = Chrom_from_string(chr_string,mitochondrial_string,/*order*/universal_coord,circularp, in store_accession()
452 bool revcompp, circularp; in process_sequence_aux() local
556 circularp = false; in process_sequence_aux()
583 circularp = true; in process_sequence_aux()
659 *seglength,/*contigtype*/0,universal_coord,circularp, in process_sequence_aux()
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| H A D | chimera.c | 484 int queryntlength, int chimera_slop, bool *circularp, bool localp) { in Chimera_bestpath() argument
531 if (circularp != NULL && circularp[Stage3_chrnum(stage3array_sub1[i])] == true) { in Chimera_bestpath()
535 if (circularp != NULL && circularp[Stage3_chrnum(stage3array_sub2[j])] == true) { in Chimera_bestpath()
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| H A D | gsnap.c | 209 static bool *circularp = NULL; variable
3027 bool *any_circular_p, bool **circularp, char *genomesubdir, char *fileroot) { in chromosome_iit_setup() argument
3050 *circularp = Univ_IIT_circularp(&(*any_circular_p),chromosome_iit); in chromosome_iit_setup()
3437 Path_solve_setup(genomelength,circularp,genomebits,genomebits_alt,regiondb,regiondb2, in worker_setup()
3442 min_intronlength,chromosome_iit,genomelength,circular_typeint,circularp, in worker_setup()
3445 Extension_search_setup(mode,chromosome_iit,genomelength,circular_typeint,circularp, in worker_setup()
3512 favor_multiexon_p,subopt_levels,circularp,altlocp,alias_starts,alias_ends, in worker_setup()
3520 expected_pairlength,pairlength_deviation,circularp,merge_samechr_p); in worker_setup()
3615 if (circularp != NULL) { in worker_cleanup()
3616 FREE(circularp); in worker_cleanup()
[all …]
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| H A D | concordance.c | 31 static bool *circularp; variable
453 if (circularp[hit5->effective_chrnum] == true) { in do_genome_plus()
585 if (circularp[hit3->effective_chrnum] == true) { in do_genome_minus()
990 if (circularp[hit5->effective_chrnum] == true) { in do_distant_plus_plus()
1140 if (circularp[hit3->effective_chrnum] == true) { in do_distant_minus_minus()
1288 if (circularp[hit5->effective_chrnum] == true) { in do_distant_plus_minus()
1408 if (circularp[hit3->effective_chrnum] == true) { in do_distant_minus_plus()
1861 circularp = circularp_in; in Concordance_setup()
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| H A D | get-genome.c | 943 bool *circularp = NULL; in main() local
1068 circularp = Univ_IIT_circularp(&any_circular_p,chromosome_iit); in main()
1086 if (circularp[indx] == true) { in main()
1208 circularp = Univ_IIT_circularp(&any_circular_p,chromosome_iit); in main()
1234 if (add_circular_p == true && circularp[indx] == true) { in main()
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| H A D | iit-read-univ.c | 235 bool *circularp; in Univ_IIT_circularp() local
241 circularp = (bool *) CALLOC(nchromosomes+1,sizeof(bool)); in Univ_IIT_circularp()
244 circularp[0] = false; /* chrnum of 0 indicates translocation */ in Univ_IIT_circularp()
250 circularp[chrnum+1] = true; in Univ_IIT_circularp()
255 return circularp; in Univ_IIT_circularp()
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| H A D | gmap.c | 200 static bool *circularp = NULL; variable
3406 CHIMERA_SLOP,circularp,/*localp*/false) == false) { in check_for_chimera()
4340 if (circularp[chrnum] == false) { in apply_stage3()
6973 circularp = (bool *) MALLOC(1*sizeof(bool)); in main()
6974 circularp[0] = false; in main()
6978 circularp = (bool *) MALLOC(1*sizeof(bool)); in main()
6979 circularp[0] = false; in main()
6992 circularp = Univ_IIT_circularp(&any_circular_p,chromosome_iit); in main()
7027 donor_typeint,acceptor_typeint,splicesites,circularp,altlocp,alias_starts,alias_ends, in main()
7286 if (circularp != NULL) { in main()
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| H A D | path-solve.c | 81 static bool *circularp; variable
642 if ((Chrpos_T) nindels < min_intronlength || splicingp == false || circularp[chrnum] == true) { in attach_qstart_diagonal()
1636 if ((Chrpos_T) nindels < min_intronlength || splicingp == false || circularp[chrnum] == true) { in attach_qend_diagonal()
3238 if (circularp[chrnum] == true) { in compute_qstart_local()
3261 if (circularp[chrnum] == true) { in compute_qstart_local()
3367 if (circularp[chrnum] == true) { in compute_qend_local()
3391 if (circularp[chrnum] == true) { in compute_qend_local()
4018 circularp = circularp_in; in Path_solve_setup()
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| H A D | samprint.c | 490 bool circularp, bool supplementaryp) { in print_substrings() argument
854 if (circularp == true) { in print_substrings()
1309 if (circularp == true) { in print_splice()
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| H A D | extension-search.c | 104 static bool *circularp; variable
144 circularp = circularp_in; in Extension_search_setup()
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| H A D | stage3hr.c | 227 static bool *circularp; variable
316 circularp = circularp_in; in Stage3hr_setup()
3459 if (circularp[hit->chrnum] == false) { in compute_circularpos()
9596 if (circularp[hit5->effective_chrnum] == true) { in Stage3_determine_pairtype()
9617 if (circularp[hit3->effective_chrnum] == true) { in Stage3_determine_pairtype()
9652 return this->circularp; in Stage3pair_circularp()
10022 if (stage3pair->circularp == true) { in Stage3pair_print_end()
10203 if (stage3pair->circularp == true) { in Stage3pair_print_end()
11694 } else if (circularp[hit5->effective_chrnum] == true) { in Stage3pair_new()
11785 new->circularp = false; in Stage3pair_new()
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| H A D | kmer-search.c | 178 static bool *circularp; variable
5338 } else if (circularp[chrnum] == true) { in combine_ends_plus()
5459 } else if (circularp[chrnum] == true) { in combine_ends_plus()
5867 } else if (circularp[chrnum] == true) { in combine_ends_minus()
5988 } else if (circularp[chrnum] == true) { in combine_ends_minus()
6869 circularp = circularp_in; in Kmer_search_setup()
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| H A D | pair.c | 6441 bool watsonp, bool first_read_p, bool circularp) {
6453 if (circularp == true) {
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| H A D | stage3.c | 328 static bool *circularp; variable
389 circularp = circularp_in; in Stage3_setup()
14196 if (circularp[chrnum] == true) { in path_compute_final()
15946 if (circularp[chrnum] == true) { in Stage3_compute_ends()
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| /dports/biology/gmap/gmap-2020-09-12/util/ |
| H A D | gmap_cat.pl.in | 121 $circularp = 1;
123 $circularp = 0;
140 if ($circularp == 1) {
150 if ($circularp == 1) {
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| H A D | gmap_process.pl.in | 123 $circularp{$contig} = 1;
211 if (defined($circularp{$contig})) {
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| H A D | fa_coords.pl.in | 34 $circularp{$chr} = 1;
41 $circularp{$chr} = 1;
336 if (defined($circularp{$chr})) {
525 if (defined($circularp{$chr})) {
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| /dports/databases/pgloader3/alexandria-20200925-git/alexandria-1/ |
| H A D | lists.lisp | 150 (labels ((circularp (object seen)
163 (circularp elt (cons object seen))))))))))
164 (circularp object nil)))
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| /dports/devel/cl-alexandria/alexandria-f35e232ceb2ada8d10e7fdf27ccac07f781eea0e/alexandria-1/ |
| H A D | lists.lisp | 150 (labels ((circularp (object seen)
163 (circularp elt (cons object seen))))))))))
164 (circularp object nil)))
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| /dports/lang/sbcl/sbcl-1.3.13/src/code/ |
| H A D | early-extensions.lisp | 174 (circularp object seen depth)))
176 (circularp (list seen depth)
191 (circularp x (list x) 0))))
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| /dports/biology/gmap/gmap-2020-09-12/ |
| H A D | ChangeLog | 2361 circularp for usersegment
9991 * stage3hr.c: Using fact that circularp[0] == false to handle translocations
10001 * stage3hr.c, stage3hr.h: Using information about circularp in
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