| /dports/biology/subread/subread-2.0.2-source/src/ |
| H A D | gene-value-index.h | 27 int gvindex_init(gene_value_index_t * index, unsigned int start_point, unsigned int all_bases_estm);
29 void gvindex_set (gene_value_index_t * index, gehash_data_t offset, gehash_key_t base_value, int pa…
31 int gvindex_dump(gene_value_index_t * index, const char filename []);
33 int gvindex_load(gene_value_index_t * index, const char filename []);
35 void gvindex_destory(gene_value_index_t * index);
37 void gvindex_baseno2offset(unsigned int base_number, gene_value_index_t * index, unsigned int * off…
40 int gvindex_match(gene_value_index_t * index, gehash_data_t offset, gehash_key_t base_value);
42 int gvindex_match_base(gene_value_index_t * index, gehash_data_t offset, const char base_int_value);
44 int gvindex_get(gene_value_index_t * index, gehash_data_t offset);
46 int match_chro(char * read, gene_value_index_t * index, unsigned int pos, int test_len, int is_nega…
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| H A D | gene-algorithms.h | 59 …uality, int is_counterpart, short mask, char * max_indel_recorder, gene_value_index_t * array_inde…
90 …t * max_vote, short *max_mask, gene_quality_score_t * max_quality, gene_value_index_t * my_array_i…
92 …t char read_str[], int read_len, unsigned int potential_position, gene_value_index_t * my_array_i…
96 int dynamic_align(char * read, int read_len, gene_value_index_t * index, unsigned int begin_positio…
98 int window_indel_align(char * read, int read_len, gene_value_index_t * index, unsigned int begin_po…
100 …_allvote_t* allvote, int qid , int pos, char * max_indel_recorder, gene_value_index_t * array_inde…
102 …quality, int is_counterpart, char mask, char * max_indel_recorder, gene_value_index_t * array_inde…
106 float final_mapping_quality(gene_value_index_t *array_index, unsigned int pos, char * read_txt, cha…
135 float match_base_quality(gene_value_index_t *array_index, char * read_txt, unsigned int pos, char …
136 int match_chro_indel(char * read, gene_value_index_t * index, unsigned int pos, int test_len, int i…
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| H A D | gene-value-index.c | 29 int gvindex_init(gene_value_index_t * index, unsigned int start_point, unsigned int total_bases_est… in gvindex_init()
56 int is_offset_in_chro(gene_value_index_t * offsets, gehash_data_t linear){ in is_offset_in_chro()
96 int gvindex_get(gene_value_index_t * index, gehash_data_t offset) in gvindex_get()
109 int gvindex_match(gene_value_index_t * index, gehash_data_t offset, gehash_key_t base_values) in gvindex_match()
135 void gvindex_set(gene_value_index_t * index, gehash_data_t offset, gehash_key_t base_values, int pa… in gvindex_set()
168 int gvindex_dump(gene_value_index_t * index, const char filename []) in gvindex_dump()
190 int gvindex_load(gene_value_index_t * index, const char filename []) in gvindex_load()
192 memset(index,0, sizeof(gene_value_index_t)); in gvindex_load()
1095 int gvindex_match_base(gene_value_index_t * index, gehash_data_t offset, const char base_int_value) in gvindex_match_base()
1112 void gvindex_destory(gene_value_index_t * index) in gvindex_destory()
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| H A D | core.h | 478 gene_value_index_t * current_value_index;
501 gene_value_index_t * current_value_index;
502 gene_value_index_t all_value_indexes[100];
655 gene_value_index_t * find_current_value_index(global_context_t * global_context, unsigned int pos, …
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| H A D | gene-algorithms.c | 974 …_allvote_t* allvote, int qid , int pos, char * max_indel_recorder, gene_value_index_t * array_inde… in explain_indel_in_middle()
1191 int match_chro_indel(char * read, gene_value_index_t * index, unsigned int pos, int test_len, int i… in match_chro_indel()
1218 int match_chro_indel_old(char * read, gene_value_index_t * index, unsigned int pos, int test_len, i… in match_chro_indel_old()
1234 …r * read_str, int read_len, gene_vote_t * dest, gene_vote_t * src, gene_value_index_t * my_array_i… in mark_votes_array_index()
1598 …t char read_str[], int read_len, unsigned int potential_position, gene_value_index_t * my_array_i… in match_read()
1714 int search_DP_branch(char * read, int read_len, gene_value_index_t * index, unsigned int begin_posi… in search_DP_branch()
1790 int window_indel_align(char * read, int read_len, gene_value_index_t * index, unsigned int begin_po… in window_indel_align()
1900 int dynamic_align(char * read, int read_len, gene_value_index_t * index, unsigned int begin_positio… in dynamic_align()
2173 float match_base_quality_cs(gene_value_index_t *array_index, char * read_txt, unsigned int pos, ch… in match_base_quality_cs()
2202 float match_base_quality(gene_value_index_t *array_index, char * read_txt, unsigned int pos, char … in match_base_quality()
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| H A D | fullscan.c | 104 gene_value_index_t index; in full_scan_read()
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| H A D | SUBindel.c | 99 memset( context->all_value_indexes , 0 , 100 * sizeof(gene_value_index_t)); in load_global_context_forindel()
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| H A D | input-files.h | 268 …n_chromosomes, int is_sequence_needed, int base_ignored_head_tail, gene_value_index_t *array_index…
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| H A D | core-indel.c | 1585 int core_extend_covered_region_15(global_context_t * global_context, gene_value_index_t *array_inde… in core_extend_covered_region_15()
1655 int core_extend_covered_region_13(gene_value_index_t *array_index, unsigned int read_start_pos, cha… in core_extend_covered_region_13()
1870 …gene_value_index_t * current_value_index = thread_context?thread_context->current_value_index:glob… in find_new_indels()
1963 …gene_value_index_t * current_value_index = thread_context?thread_context->current_value_index:glob… in find_new_indels()
2291 …gene_value_index_t * current_index = find_current_value_index(global_context , event_body -> event… in write_indel_final_results()
2441 gene_value_index_t * base_index = &global_context->all_value_indexes[0] ; in write_local_reassembly()
2661 gene_value_index_t * base_index = &global_context->all_value_indexes[0] ; in finalise_db_graph()
3467 int find_best_location_for_probe(global_context_t * global_context ,gene_value_index_t * base_index… in find_best_location_for_probe()
3519 gene_value_index_t * base_index = &global_context->all_value_indexes[0] ; in find_potential_ultralong_indels()
4074 gene_value_index_t * base_index = &global_context->all_value_indexes[0] ; in finalise_pileup_file_by_voting()
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| H A D | subread.h | 309 } gene_value_index_t; typedef
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| H A D | index-builder.c | 88 gene_value_index_t value_array_index; in build_gene_index()
124 memset(&value_array_index, 0, sizeof(gene_value_index_t)); in build_gene_index()
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| H A D | core-junction.c | 144 …gene_value_index_t * value_index = thread_context?thread_context->current_value_index:global_conte… in search_events_to_front()
602 …gene_value_index_t * value_index = thread_context?thread_context->current_value_index:global_conte… in search_events_to_back()
1589 …gene_value_index_t * value_index = thread_context?thread_context->current_value_index:global_conte… in extend_uncovered_region_juncs()
2060 …gene_value_index_t * value_index = thread_context?thread_context->current_value_index:global_conte… in find_donor_receptor()
2893 …gene_value_index_t * current_value_index = thread_context?thread_context->current_value_index:glob… in final_CIGAR_quality()
3564 …gene_value_index_t * value_index = thread_context?thread_context->current_value_index:global_conte… in donor_jumped_score()
3665 …gene_value_index_t * value_index = thread_context?thread_context->current_value_index:global_conte… in donor_score()
4173 …gene_value_index_t * current_index = find_current_value_index(global_context , event_body -> event… in write_fusion_final_results()
4346 void get_chro_2base(char *buf, gene_value_index_t * index, unsigned int pos, int is_negative_strand) in get_chro_2base()
4377 …gene_value_index_t * base_index = thread_context?thread_context->current_value_index:global_contex… in core_search_short_exons()
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| H A D | SNPCalling.c | 90 gene_value_index_t * subread_index_array;
1415 parameters -> subread_index_array = (gene_value_index_t*) malloc(sizeof(gene_value_index_t)); in SNP_calling()
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| H A D | core.c | 2226 gene_value_index_t * find_current_value_index(global_context_t * global_context, unsigned int pos, …
3304 …gene_value_index_t * curr_val_index = thread_context? thread_context -> current_value_index: globa…
4240 memset( context->all_value_indexes , 0 , 100 * sizeof(gene_value_index_t));
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| H A D | input-files.c | 1835 …n_chromosomes, int is_sequence_needed, int base_ignored_head_tail, gene_value_index_t *array_index… in break_SAM_file()
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