Lines Matching refs:thread_contexts
276 fc_thread_thread_context_t * thread_contexts; member
1811 global_context -> thread_contexts[xk1].count_table[xk2] = 0; in process_pairer_reset()
1814 global_context -> thread_contexts[xk1].del4_added_reads = 0; in process_pairer_reset()
1816 global_context -> thread_contexts[xk1].all_reads = 0; in process_pairer_reset()
1817 global_context -> thread_contexts[xk1].nreads_mapped_to_exon = 0; in process_pairer_reset()
1819 global_context -> thread_contexts[xk1].read_counters.unassigned_ambiguous = 0; in process_pairer_reset()
1820 global_context -> thread_contexts[xk1].read_counters.unassigned_nofeatures = 0; in process_pairer_reset()
1821 global_context -> thread_contexts[xk1].read_counters.unassigned_unmapped = 0; in process_pairer_reset()
1822 global_context -> thread_contexts[xk1].read_counters.unassigned_singleton = 0; in process_pairer_reset()
1823 global_context -> thread_contexts[xk1].read_counters.unassigned_read_type = 0; in process_pairer_reset()
1824 global_context -> thread_contexts[xk1].read_counters.unassigned_mappingquality = 0; in process_pairer_reset()
1825 global_context -> thread_contexts[xk1].read_counters.unassigned_fragmentlength = 0; in process_pairer_reset()
1826 global_context -> thread_contexts[xk1].read_counters.unassigned_chimericreads = 0; in process_pairer_reset()
1827 global_context -> thread_contexts[xk1].read_counters.unassigned_multimapping = 0; in process_pairer_reset()
1828 global_context -> thread_contexts[xk1].read_counters.unassigned_secondary = 0; in process_pairer_reset()
1829 global_context -> thread_contexts[xk1].read_counters.unassigned_junction_condition = 0; in process_pairer_reset()
1830 global_context -> thread_contexts[xk1].read_counters.unassigned_duplicate = 0; in process_pairer_reset()
1831 global_context -> thread_contexts[xk1].read_counters.unassigned_overlapping_length = 0; in process_pairer_reset()
1832 global_context -> thread_contexts[xk1].read_counters.assigned_reads = 0; in process_pairer_reset()
1833 global_context -> thread_contexts[xk1].read_details_buff_used = 0; in process_pairer_reset()
1837 HashTableDestroy(global_context -> thread_contexts[xk1].junction_counting_table); in process_pairer_reset()
1838 global_context -> thread_contexts[xk1].junction_counting_table = HashTableCreate(131317); in process_pairer_reset()
1839 …HashTableSetHashFunction(global_context -> thread_contexts[xk1].junction_counting_table,HashTableS… in process_pairer_reset()
1840 …HashTableSetDeallocationFunctions(global_context -> thread_contexts[xk1].junction_counting_table, … in process_pairer_reset()
1841 …HashTableSetKeyComparisonFunction(global_context -> thread_contexts[xk1].junction_counting_table, … in process_pairer_reset()
1843 HashTableDestroy(global_context -> thread_contexts[xk1].splicing_point_table); in process_pairer_reset()
1844 global_context -> thread_contexts[xk1].splicing_point_table = HashTableCreate(131317); in process_pairer_reset()
1845 …HashTableSetHashFunction(global_context -> thread_contexts[xk1].splicing_point_table,HashTableStri… in process_pairer_reset()
1846 …HashTableSetDeallocationFunctions(global_context -> thread_contexts[xk1].splicing_point_table, fre… in process_pairer_reset()
1847 …HashTableSetKeyComparisonFunction(global_context -> thread_contexts[xk1].splicing_point_table, fc_… in process_pairer_reset()
1851 HashTableDestroy(global_context -> thread_contexts[xk1].RG_table); in process_pairer_reset()
1852 global_context -> thread_contexts[xk1].RG_table = HashTableCreate(97); in process_pairer_reset()
1853 …HashTableSetHashFunction(global_context -> thread_contexts[xk1].RG_table,HashTableStringHashFuncti… in process_pairer_reset()
1854 …HashTableSetDeallocationFunctions(global_context -> thread_contexts[xk1].RG_table, free, disalloca… in process_pairer_reset()
1855 …HashTableSetKeyComparisonFunction(global_context -> thread_contexts[xk1].RG_table, fc_strcmp_chro); in process_pairer_reset()
2181 fc_thread_thread_context_t * thread_context = global_context -> thread_contexts; in process_pairer_header()
2256 fc_thread_thread_context_t * RGthread_context = global_context -> thread_contexts + thread_no; in process_pairer_header()
2912 fc_thread_thread_context_t * thread_context = global_context -> thread_contexts + thread_no; in process_pairer_scRNAr2_output()
2921 fc_thread_thread_context_t * thread_context = global_context -> thread_contexts + thread_no; in process_pairer_output()
5818 mapped_reads += global_context -> thread_contexts[thrid].scRNA_mapped_reads_per_sample[x1]; in scRNA_merged_to_tables_write()
5819 assigned_reads += global_context -> thread_contexts[thrid].scRNA_assigned_reads_per_sample[x1]; in scRNA_merged_to_tables_write()
5820 all_reads += global_context -> thread_contexts[thrid].scRNA_reads_per_sample[x1]; in scRNA_merged_to_tables_write()
6072 vpp[1] = global_context -> thread_contexts+xk1; in fc_thread_merge_results()
6326 HashTable * thread_rg_tab = global_context -> thread_contexts[xk1].RG_table; in fc_thread_merge_results()
6336 …rg_old_tabs[0] = calloc(global_context -> thread_contexts[xk1].count_table_size, sizeof(srInt_64)); in fc_thread_merge_results()
6424 nreads[xk2]+=global_context -> thread_contexts[xk1].count_table[xk2]; in fc_thread_merge_results()
6426 total_input_reads += global_context -> thread_contexts[xk1].all_reads; in fc_thread_merge_results()
6427 (*nreads_mapped_to_exon) += global_context -> thread_contexts[xk1].nreads_mapped_to_exon; in fc_thread_merge_results()
6429 …global_context -> read_counters.unassigned_ambiguous += global_context -> thread_contexts[xk1].rea… in fc_thread_merge_results()
6430 …global_context -> read_counters.unassigned_nofeatures += global_context -> thread_contexts[xk1].re… in fc_thread_merge_results()
6431 … -> read_counters.unassigned_overlapping_length += global_context -> thread_contexts[xk1].read_cou… in fc_thread_merge_results()
6432 …global_context -> read_counters.unassigned_unmapped += global_context -> thread_contexts[xk1].read… in fc_thread_merge_results()
6433 …global_context -> read_counters.unassigned_singleton += global_context -> thread_contexts[xk1].rea… in fc_thread_merge_results()
6434 …global_context -> read_counters.unassigned_read_type += global_context -> thread_contexts[xk1].rea… in fc_thread_merge_results()
6435 …global_context -> read_counters.unassigned_mappingquality += global_context -> thread_contexts[xk1… in fc_thread_merge_results()
6436 …global_context -> read_counters.unassigned_fragmentlength += global_context -> thread_contexts[xk1… in fc_thread_merge_results()
6437 …global_context -> read_counters.unassigned_chimericreads += global_context -> thread_contexts[xk1]… in fc_thread_merge_results()
6438 …global_context -> read_counters.unassigned_multimapping += global_context -> thread_contexts[xk1].… in fc_thread_merge_results()
6439 …global_context -> read_counters.unassigned_secondary += global_context -> thread_contexts[xk1].rea… in fc_thread_merge_results()
6440 … -> read_counters.unassigned_junction_condition += global_context -> thread_contexts[xk1].read_cou… in fc_thread_merge_results()
6441 …global_context -> read_counters.unassigned_duplicate += global_context -> thread_contexts[xk1].rea… in fc_thread_merge_results()
6442 …global_context -> read_counters.assigned_reads += global_context -> thread_contexts[xk1].read_coun… in fc_thread_merge_results()
6444 …my_read_counter->unassigned_ambiguous += global_context -> thread_contexts[xk1].read_counters.unas… in fc_thread_merge_results()
6445 …my_read_counter->unassigned_nofeatures += global_context -> thread_contexts[xk1].read_counters.una… in fc_thread_merge_results()
6446 …my_read_counter->unassigned_overlapping_length += global_context -> thread_contexts[xk1].read_coun… in fc_thread_merge_results()
6447 …my_read_counter->unassigned_unmapped += global_context -> thread_contexts[xk1].read_counters.unass… in fc_thread_merge_results()
6448 …my_read_counter->unassigned_singleton += global_context -> thread_contexts[xk1].read_counters.unas… in fc_thread_merge_results()
6449 …my_read_counter->unassigned_read_type += global_context -> thread_contexts[xk1].read_counters.unas… in fc_thread_merge_results()
6450 …my_read_counter->unassigned_mappingquality += global_context -> thread_contexts[xk1].read_counters… in fc_thread_merge_results()
6451 …my_read_counter->unassigned_fragmentlength += global_context -> thread_contexts[xk1].read_counters… in fc_thread_merge_results()
6452 …my_read_counter->unassigned_chimericreads += global_context -> thread_contexts[xk1].read_counters.… in fc_thread_merge_results()
6453 …my_read_counter->unassigned_multimapping += global_context -> thread_contexts[xk1].read_counters.u… in fc_thread_merge_results()
6454 …my_read_counter->unassigned_secondary += global_context -> thread_contexts[xk1].read_counters.unas… in fc_thread_merge_results()
6455 …my_read_counter->unassigned_junction_condition += global_context -> thread_contexts[xk1].read_coun… in fc_thread_merge_results()
6456 …my_read_counter->unassigned_duplicate += global_context -> thread_contexts[xk1].read_counters.unas… in fc_thread_merge_results()
6457 …my_read_counter->assigned_reads += global_context -> thread_contexts[xk1].read_counters.assigned_r… in fc_thread_merge_results()
6461 …for(bucket_i = 0 ; bucket_i < global_context -> thread_contexts[xk1].junction_counting_table -> nu… in fc_thread_merge_results()
6463 … cursor = global_context -> thread_contexts[xk1].junction_counting_table -> bucketArray[bucket_i]; in fc_thread_merge_results()
6478 …for(bucket_i = 0 ; bucket_i < global_context -> thread_contexts[xk1].splicing_point_table -> numOf… in fc_thread_merge_results()
6480 cursor = global_context -> thread_contexts[xk1].splicing_point_table -> bucketArray[bucket_i]; in fc_thread_merge_results()
6932 …global_context -> thread_contexts = malloc(sizeof(fc_thread_thread_context_t) * global_context -> … in fc_thread_start_threads()
6936 global_context -> thread_contexts[xk1].thread_id = xk1; in fc_thread_start_threads()
6937 global_context -> thread_contexts[xk1].chunk_read_ptr = 0; in fc_thread_start_threads()
6938 global_context -> thread_contexts[xk1].count_table = calloc(sizeof(read_count_type_t), et_exons); in fc_thread_start_threads()
6939 global_context -> thread_contexts[xk1].count_table_size = et_exons; in fc_thread_start_threads()
6940 global_context -> thread_contexts[xk1].nreads_mapped_to_exon = 0; in fc_thread_start_threads()
6941 global_context -> thread_contexts[xk1].all_reads = 0; in fc_thread_start_threads()
6942 global_context -> thread_contexts[xk1].chro_name_buff = malloc(CHROMOSOME_NAME_LENGTH); in fc_thread_start_threads()
6944 global_context -> thread_contexts[xk1].read_counters.assigned_reads = 0; in fc_thread_start_threads()
6945 global_context -> thread_contexts[xk1].read_counters.unassigned_ambiguous = 0; in fc_thread_start_threads()
6946 global_context -> thread_contexts[xk1].read_counters.unassigned_nofeatures = 0; in fc_thread_start_threads()
6947 global_context -> thread_contexts[xk1].read_counters.unassigned_unmapped = 0; in fc_thread_start_threads()
6948 global_context -> thread_contexts[xk1].read_counters.unassigned_singleton = 0; in fc_thread_start_threads()
6949 global_context -> thread_contexts[xk1].read_counters.unassigned_read_type = 0; in fc_thread_start_threads()
6950 global_context -> thread_contexts[xk1].read_counters.unassigned_mappingquality = 0; in fc_thread_start_threads()
6951 global_context -> thread_contexts[xk1].read_counters.unassigned_fragmentlength = 0; in fc_thread_start_threads()
6952 global_context -> thread_contexts[xk1].read_counters.unassigned_chimericreads = 0; in fc_thread_start_threads()
6953 global_context -> thread_contexts[xk1].read_counters.unassigned_multimapping = 0; in fc_thread_start_threads()
6954 global_context -> thread_contexts[xk1].read_counters.unassigned_secondary = 0; in fc_thread_start_threads()
6955 global_context -> thread_contexts[xk1].read_counters.unassigned_junction_condition = 0; in fc_thread_start_threads()
6956 global_context -> thread_contexts[xk1].read_counters.unassigned_overlapping_length = 0; in fc_thread_start_threads()
6957 global_context -> thread_contexts[xk1].read_counters.unassigned_duplicate = 0; in fc_thread_start_threads()
6958 global_context -> thread_contexts[xk1].read_details_buff_used = 0; in fc_thread_start_threads()
6959 global_context -> thread_contexts[xk1].hits_number_capacity = 300 ; in fc_thread_start_threads()
6961 …global_context -> thread_contexts[xk1].hits_start_pos1 = malloc(sizeof(int)* global_context -> thr… in fc_thread_start_threads()
6962 …global_context -> thread_contexts[xk1].hits_start_pos2 = malloc(sizeof(int)* global_context -> thr… in fc_thread_start_threads()
6963 …global_context -> thread_contexts[xk1].hits_length1 = malloc(sizeof(short)* global_context -> thre… in fc_thread_start_threads()
6964 …global_context -> thread_contexts[xk1].hits_length2 = malloc(sizeof(short)* global_context -> thre… in fc_thread_start_threads()
6965 …global_context -> thread_contexts[xk1].hits_chro1 = malloc(sizeof(char*)* global_context -> thread… in fc_thread_start_threads()
6966 …global_context -> thread_contexts[xk1].hits_chro2 = malloc(sizeof(char*)* global_context -> thread… in fc_thread_start_threads()
6967 …global_context -> thread_contexts[xk1].hits_indices1 = malloc(sizeof(srInt_64)* global_context -> … in fc_thread_start_threads()
6968 …global_context -> thread_contexts[xk1].hits_indices2 = malloc(sizeof(srInt_64)* global_context -> … in fc_thread_start_threads()
6970 …global_context -> thread_contexts[xk1].scoring_buff_numbers = malloc(sizeof(int)* global_context -… in fc_thread_start_threads()
6971 …global_context -> thread_contexts[xk1].scoring_buff_flags = malloc(sizeof(int)* global_context -> … in fc_thread_start_threads()
6972 …global_context -> thread_contexts[xk1].scoring_buff_overlappings = malloc(sizeof(int)* global_cont… in fc_thread_start_threads()
6973 …global_context -> thread_contexts[xk1].scoring_buff_exon_ids =malloc(sizeof(srInt_64)* global_cont… in fc_thread_start_threads()
6976 …global_context -> thread_contexts[xk1].read_details_buff = malloc(70000 + 2 * MAX_FC_READ_LENGTH *… in fc_thread_start_threads()
6977 …global_context -> thread_contexts[xk1].bam_compressed_buff = malloc(70000 + 2 * MAX_FC_READ_LENGTH… in fc_thread_start_threads()
6981 …global_context -> thread_contexts[xk1].scoring_buff_gap_chros = malloc( sizeof(char *) * global_co… in fc_thread_start_threads()
6982 …global_context -> thread_contexts[xk1].scoring_buff_gap_starts = malloc( sizeof(unsigned int ) * g… in fc_thread_start_threads()
6983 …global_context -> thread_contexts[xk1].scoring_buff_gap_lengths = malloc( sizeof(unsigned short) *… in fc_thread_start_threads()
6984 } else global_context -> thread_contexts[xk1].scoring_buff_gap_chros = NULL; in fc_thread_start_threads()
6988 global_context -> thread_contexts[xk1].junction_counting_table = HashTableCreate(131317); in fc_thread_start_threads()
6989 …HashTableSetHashFunction(global_context -> thread_contexts[xk1].junction_counting_table,HashTableS… in fc_thread_start_threads()
6990 …HashTableSetDeallocationFunctions(global_context -> thread_contexts[xk1].junction_counting_table, … in fc_thread_start_threads()
6991 …HashTableSetKeyComparisonFunction(global_context -> thread_contexts[xk1].junction_counting_table, … in fc_thread_start_threads()
6993 global_context -> thread_contexts[xk1].splicing_point_table = HashTableCreate(131317); in fc_thread_start_threads()
6994 …HashTableSetHashFunction(global_context -> thread_contexts[xk1].splicing_point_table,HashTableStri… in fc_thread_start_threads()
6995 …HashTableSetDeallocationFunctions(global_context -> thread_contexts[xk1].splicing_point_table, fre… in fc_thread_start_threads()
6996 …HashTableSetKeyComparisonFunction(global_context -> thread_contexts[xk1].splicing_point_table, fc_… in fc_thread_start_threads()
7000 global_context -> thread_contexts[xk1].RG_table = HashTableCreate(97); in fc_thread_start_threads()
7001 …HashTableSetHashFunction(global_context -> thread_contexts[xk1].RG_table,HashTableStringHashFuncti… in fc_thread_start_threads()
7002 …HashTableSetDeallocationFunctions(global_context -> thread_contexts[xk1].RG_table, free, disalloca… in fc_thread_start_threads()
7003 …HashTableSetKeyComparisonFunction(global_context -> thread_contexts[xk1].RG_table, fc_strcmp_chro); in fc_thread_start_threads()
7007 …global_context -> thread_contexts[xk1].scRNA_reads_per_sample = calloc(sizeof(srInt_64),global_con… in fc_thread_start_threads()
7008 …global_context -> thread_contexts[xk1].scRNA_mapped_reads_per_sample = calloc(sizeof(srInt_64),glo… in fc_thread_start_threads()
7009 …global_context -> thread_contexts[xk1].scRNA_assigned_reads_per_sample = calloc(sizeof(srInt_64),g… in fc_thread_start_threads()
7010 …global_context -> thread_contexts[xk1].scRNA_sample_bc_tables = malloc(sizeof(HashTable*) * global… in fc_thread_start_threads()
7011 global_context -> thread_contexts[xk1].scRNA_registered_UMI_table = StringTableCreate(100000); in fc_thread_start_threads()
7012 …HashTableSetDeallocationFunctions(global_context -> thread_contexts[xk1].scRNA_registered_UMI_tab… in fc_thread_start_threads()
7018 global_context -> thread_contexts[xk1].scRNA_sample_bc_tables[xk2] = al; in fc_thread_start_threads()
7020 global_context -> thread_contexts[xk1].scRNA_pooled_reads=0; in fc_thread_start_threads()
7021 global_context -> thread_contexts[xk1].scRNA_has_valid_sample_index =0; in fc_thread_start_threads()
7022 global_context -> thread_contexts[xk1].scRNA_has_valid_cell_barcode =0; in fc_thread_start_threads()
7025 if(!global_context -> thread_contexts[xk1].count_table) return 1; in fc_thread_start_threads()
7047 write_read_detailed_remainder(global_context, global_context -> thread_contexts+xk1); in fc_thread_destroy_thread_context()
7052 …int tail_size = compress_read_detail_BAM( global_context, global_context -> thread_contexts, 0,0,b… in fc_thread_destroy_thread_context()
7064 free(global_context -> thread_contexts[xk1].count_table); in fc_thread_destroy_thread_context()
7065 free(global_context -> thread_contexts[xk1].chro_name_buff); in fc_thread_destroy_thread_context()
7066 free(global_context -> thread_contexts[xk1].hits_start_pos1); in fc_thread_destroy_thread_context()
7067 free(global_context -> thread_contexts[xk1].hits_start_pos2); in fc_thread_destroy_thread_context()
7068 free(global_context -> thread_contexts[xk1].hits_length1); in fc_thread_destroy_thread_context()
7069 free(global_context -> thread_contexts[xk1].hits_length2); in fc_thread_destroy_thread_context()
7070 free(global_context -> thread_contexts[xk1].hits_chro1); in fc_thread_destroy_thread_context()
7071 free(global_context -> thread_contexts[xk1].hits_chro2); in fc_thread_destroy_thread_context()
7072 free(global_context -> thread_contexts[xk1].hits_indices1); in fc_thread_destroy_thread_context()
7073 free(global_context -> thread_contexts[xk1].hits_indices2); in fc_thread_destroy_thread_context()
7074 free(global_context -> thread_contexts[xk1].scoring_buff_numbers); in fc_thread_destroy_thread_context()
7075 free(global_context -> thread_contexts[xk1].scoring_buff_flags); in fc_thread_destroy_thread_context()
7076 free(global_context -> thread_contexts[xk1].scoring_buff_overlappings); in fc_thread_destroy_thread_context()
7077 free(global_context -> thread_contexts[xk1].scoring_buff_exon_ids); in fc_thread_destroy_thread_context()
7079 if(global_context -> thread_contexts[xk1].scoring_buff_gap_chros){ in fc_thread_destroy_thread_context()
7080 free(global_context -> thread_contexts[xk1].scoring_buff_gap_chros); in fc_thread_destroy_thread_context()
7081 free(global_context -> thread_contexts[xk1].scoring_buff_gap_starts); in fc_thread_destroy_thread_context()
7082 free(global_context -> thread_contexts[xk1].scoring_buff_gap_lengths); in fc_thread_destroy_thread_context()
7085 HashTableDestroy(global_context -> thread_contexts[xk1].junction_counting_table); in fc_thread_destroy_thread_context()
7086 HashTableDestroy(global_context -> thread_contexts[xk1].splicing_point_table); in fc_thread_destroy_thread_context()
7089 HashTableDestroy(global_context -> thread_contexts[xk1].RG_table); in fc_thread_destroy_thread_context()
7091 free(global_context -> thread_contexts[xk1].read_details_buff); in fc_thread_destroy_thread_context()
7092 free(global_context -> thread_contexts[xk1].bam_compressed_buff); in fc_thread_destroy_thread_context()
7098 HashTableDestroy(global_context -> thread_contexts[xk1].scRNA_sample_bc_tables[xk2]); in fc_thread_destroy_thread_context()
7101 free(global_context -> thread_contexts[xk1].scRNA_reads_per_sample); in fc_thread_destroy_thread_context()
7102 free(global_context -> thread_contexts[xk1].scRNA_mapped_reads_per_sample); in fc_thread_destroy_thread_context()
7103 free(global_context -> thread_contexts[xk1].scRNA_assigned_reads_per_sample); in fc_thread_destroy_thread_context()
7104 free(global_context -> thread_contexts[xk1].scRNA_sample_bc_tables); in fc_thread_destroy_thread_context()
7105 HashTableDestroy(global_context -> thread_contexts[xk1].scRNA_registered_UMI_table); in fc_thread_destroy_thread_context()
7109 free(global_context -> thread_contexts); in fc_thread_destroy_thread_context()