/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | oligoindex_hr.h | 90 typedef struct Oligoindex_array_T *Oligoindex_array_T; typedef 99 Oligoindex_array_length (Oligoindex_array_T oligoindices); 101 Oligoindex_array_elt (Oligoindex_array_T oligoindices, int source); 103 extern Oligoindex_array_T 106 extern Oligoindex_array_T 125 Oligoindex_array_free(Oligoindex_array_T *old); 130 Oligoindex_array_T array, T this, char *queryuc_ptr,
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H A D | stage2.h | 54 int genestrand, Stage2_alloc_T stage2_alloc, Oligoindex_array_T oligoindices, 64 Oligoindex_array_T oligoindices, 74 Oligoindex_array_T oligoindices, 83 Oligoindex_array_T oligoindices, 92 Oligoindex_array_T oligoindices,
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H A D | stage3.h | 326 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, 357 …int sense_filter, Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool); 389 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, 440 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
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H A D | concordance.c | 131 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, 233 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, 334 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, 435 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in do_genome_plus() 566 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in do_genome_minus() 705 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in Concordance_pair_up_genome() 974 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in do_distant_plus_plus() 1124 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in do_distant_minus_minus() 1273 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in do_distant_plus_minus() 1393 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in do_distant_minus_plus() [all …]
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H A D | stage1hr.h | 121 Oligoindex_array_T oligoindices_minor,
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H A D | gmap.c | 1149 Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor, in update_stage3middle_list() 1253 Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor, in update_stage3list() 1441 Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor, in stage3_from_usersegment() 1763 Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor, in stage3_from_gregions() 2661 Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor, in check_for_local() 3104 Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor, in check_for_chimera() 3621 Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor, in check_middle_piece_local() 3828 Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor, in check_middle_piece_chimera() 4059 Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor, in apply_stage3() 4423 …Stage2_alloc_T stage2_alloc, Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindice… in process_request() [all …]
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H A D | stage2.c | 5829 int genestrand, Stage2_alloc_T stage2_alloc, Oligoindex_array_T oligoindices, in Stage2_scan() 6553 Oligoindex_array_T oligoindices, in Stage2_compute() 7072 Oligoindex_array_T oligoindices, in Stage2_compute_one() 7243 Oligoindex_array_T oligoindices, in Stage2_compute_starts() 7436 Oligoindex_array_T oligoindices, in Stage2_compute_ends()
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H A D | stage3.c | 11093 Oligoindex_array_T oligoindices_minor, in traverse_dual_break() 11434 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in build_dual_breaks() 12019 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in build_pairs_introns() 13531 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in path_compute_dir() 14180 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in path_compute_final() 15693 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in Stage3_compute_middle() 15846 …int sense_filter, Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool)… in Stage3_compute_ends() 16735 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in Stage3_compute_one() 18446 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in recompute_for_cdna_direction() 18546 Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, in Stage3_merge_local()
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H A D | oligoindex_hr.c | 119 struct Oligoindex_array_T { struct 8798 Oligoindex_array_length (Oligoindex_array_T oligoindices) { in Oligoindex_array_length() 8803 Oligoindex_array_elt (Oligoindex_array_T oligoindices, int source) { in Oligoindex_array_elt() 8808 Oligoindex_array_T 8810 Oligoindex_array_T new = (Oligoindex_array_T) MALLOC_KEEP(sizeof(*new)); in Oligoindex_array_new_major() 8835 Oligoindex_array_T 8837 Oligoindex_array_T new = (Oligoindex_array_T) MALLOC_KEEP(sizeof(*new)); in Oligoindex_array_new_minor() 34066 Oligoindex_array_free (Oligoindex_array_T *old) { in Oligoindex_array_free() 34143 Oligoindex_array_T array, T this, char *queryuc_ptr, in Oligoindex_get_mappings()
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H A D | gsnap.c | 929 Oligoindex_array_T oligoindices_minor, in process_request()
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H A D | stage1hr.c | 1423 Oligoindex_array_T oligoindices_minor, in Stage1_single_read()
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/dports/biology/gmap/gmap-2020-09-12/ |
H A D | ChangeLog | 7260 * oligoindex_hr.c: Freeing storage memory in Oligoindex_array_T object 7297 * oligoindex_hr.c: Allocating storage for Oligoindex_array_T 7313 Oligoindex_array_T object, which also holds storage
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