mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-04 00:18:11 +08:00
debug
This commit is contained in:
Haoyu Cheng
+31
-14
@@ -16,6 +16,9 @@ All_reads R_INF;
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pthread_mutex_t statistics;
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long long total_matched_overlap_0 = 0;
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long long total_matched_overlap_1 = 0;
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long long total_potiental_matched_overlap_0 = 0;
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long long total_potiental_matched_overlap_1 = 0;
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long long complete_threads = 0;
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@@ -689,6 +692,8 @@ void* Overlap_calculate_heap_merge(void* arg)
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long long matched_overlap_0 = 0;
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long long matched_overlap_1 = 0;
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long long potiental_matched_overlap_0 = 0;
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long long potiental_matched_overlap_1 = 0;
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long long j;
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int thr_ID = *((int*)arg);
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@@ -698,6 +703,10 @@ void* Overlap_calculate_heap_merge(void* arg)
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UC_Read g_read;
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init_UC_Read(&g_read);
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UC_Read overlap_read;
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init_UC_Read(&overlap_read);
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HPC_seq HPC_read;
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Hash_code k_code;
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uint64_t code;
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@@ -852,29 +861,30 @@ void* Overlap_calculate_heap_merge(void* arg)
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///merge_k_mer_pos_list_alloc(&array_list, &l);
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merge_k_mer_pos_list_alloc_heap_sort(&array_list, &l, &heap);
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/**
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if (array_list.length < 3)
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{
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merge_k_mer_pos_list_alloc(&array_list, &l);
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}
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else
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{
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merge_k_mer_pos_list_alloc_heap_sort_advance(&array_list, &l, &heap);
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}
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**/
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// if (array_list.length < 3)
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// {
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// merge_k_mer_pos_list_alloc(&array_list, &l);
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// }
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// else
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// {
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// merge_k_mer_pos_list_alloc_heap_sort_advance(&array_list, &l, &heap);
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// }
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///以x_pos_e，即结束位置为主元排序
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calculate_overlap_region(&l, &overlap_list, i, g_read.length, &R_INF);
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correct_overlap(&overlap_list, &R_INF, &g_read, &correct);
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correct_overlap(&overlap_list, &R_INF, &g_read, &correct, &overlap_read,
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&matched_overlap_0, &matched_overlap_1, &potiental_matched_overlap_0, &potiental_matched_overlap_1);
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/**
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for (j = 0; j < overlap_list.length; j++)
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{
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long long Len_x = overlap_list.list[j].x_pos_e - overlap_list.list[j].x_pos_s + 1;
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if (Len_x * 0.6 <= overlap_list.list[j].align_length)
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if (Len_x * 0.9 <= overlap_list.list[j].align_length)
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{
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if (overlap_list.list[j].y_pos_strand == 0)
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{
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@@ -886,6 +896,7 @@ void* Overlap_calculate_heap_merge(void* arg)
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}
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}
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}
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**/
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/**
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POA_i = 0;
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@@ -988,6 +999,8 @@ void* Overlap_calculate_heap_merge(void* arg)
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destory_Graph(&POA_Graph);
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destory_UC_Read(&g_read);
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destory_UC_Read(&overlap_read);
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destory_Correct_dumy(&correct);
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@@ -995,11 +1008,15 @@ void* Overlap_calculate_heap_merge(void* arg)
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pthread_mutex_lock(&statistics);
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total_matched_overlap_0 += matched_overlap_0;
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total_matched_overlap_1 += matched_overlap_1;
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total_potiental_matched_overlap_0 += potiental_matched_overlap_0;
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total_potiental_matched_overlap_1 += potiental_matched_overlap_1;
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complete_threads++;
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if(complete_threads == thread_num)
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{
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fprintf(stderr, "total_matched_overlap_0: %llu\n", total_matched_overlap_0);
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fprintf(stderr, "total_matched_overlap_1: %llu\n", total_matched_overlap_1);
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fprintf(stderr, "total_potiental_matched_overlap_0: %llu\n", total_potiental_matched_overlap_0);
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fprintf(stderr, "total_potiental_matched_overlap_1: %llu\n", total_potiental_matched_overlap_1);
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}
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pthread_mutex_unlock(&statistics);
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}
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+85
-1
@@ -674,7 +674,11 @@ char* r_string)
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}
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void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Read* g_read, Correct_dumy* dumy)
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void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
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UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read,
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long long* matched_overlap_0, long long* matched_overlap_1,
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long long* potiental_matched_overlap_0, long long* potiental_matched_overlap_1)
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{
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reverse_complement(g_read->seq, g_read->length);
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@@ -733,6 +737,86 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Re
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// T_total_match, T_total_unmatch, T_total_mis);
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// pthread_mutex_unlock(&debug_statistics);
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/************需要注释掉********* */
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/**
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long long j;
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long long Len_x;
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int threshold;
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long long y_start;
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long long Len_y;
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long long currentIDLen;
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for (j = 0; j < overlap_list->length; j++)
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{
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Len_x = overlap_list->list[j].x_pos_e - overlap_list->list[j].x_pos_s + 1;
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if (Len_x * 0.6 <= overlap_list->list[j].align_length)
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{
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threshold = Len_x * 0.04;
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y_start = overlap_list->list[j].y_pos_s - threshold;
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if (y_start < 0)
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{
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y_start = 0;
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}
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///当前y的长度
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currentIDLen = Get_READ_LENGTH((*R_INF), overlap_list->list[j].y_id);
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///不能超过y的剩余长度
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Len_y = MIN(Len_x + 2 * threshold, currentIDLen - y_start);
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if (overlap_list->list[j].y_pos_strand == 0)
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{
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recover_UC_Read(overlap_read, R_INF, overlap_list->list[j].y_id);
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(*matched_overlap_0)++;
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}
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else
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{
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recover_UC_Read_RC(overlap_read, R_INF, overlap_list->list[j].y_id);
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(*matched_overlap_1)++;
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}
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EdlibAlignResult result = edlibAlign(g_read->seq + overlap_list->list[j].x_pos_s, Len_x,
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overlap_read->seq + y_start, Len_y,
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edlibNewAlignConfig(threshold, EDLIB_MODE_HW, EDLIB_TASK_PATH, NULL, 0));
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if (result.status == EDLIB_STATUS_OK && result.editDistance != -1) {
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char* cigar = edlibAlignmentToCigar(result.alignment, result.alignmentLength, EDLIB_CIGAR_STANDARD);
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int cigar_length = strlen(cigar);
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free(cigar);
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if (overlap_list->list[j].y_pos_strand == 0)
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{
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(*potiental_matched_overlap_0)++;
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}
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else
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{
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(*potiental_matched_overlap_1)++;
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}
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// if (overlap_list->list[j].shared_seed == 1 && Len_x >= 1000)
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// {
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// (*matched_overlap_0)++;
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// }
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// if (overlap_list->list[j].shared_seed == 2 && Len_x >= 1000)
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// {
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// (*matched_overlap_1)++;
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// }
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}
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edlibFreeAlignResult(result);
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}
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}
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**/
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}
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@@ -26,8 +26,10 @@ typedef struct
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} Correct_dumy;
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void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Read* g_read, Correct_dumy* dumy);
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void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
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UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read,
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long long* matched_overlap_0, long long* matched_overlap_1,
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long long* potiental_matched_overlap_0, long long* potiental_matched_overlap_1);
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void init_Correct_dumy(Correct_dumy* list);
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void destory_Correct_dumy(Correct_dumy* list);
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void clear_Correct_dumy(Correct_dumy* list, overlap_region_alloc* overlap_list);
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@@ -228,6 +228,386 @@ inline int Reserve_Banded_BPM
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}
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inline int Reserve_Banded_BPM_PATH
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(char *pattern, int p_length, char *text, int t_length, unsigned short errthold,
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unsigned int* return_err, int* return_start_site, int* return_path_length, Word* matrix_bit, char* path)
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{
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(*return_err) = (unsigned int)-1;
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Word Peq[256];
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int band_length = (errthold << 1) + 1;
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int i = 0;
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Word tmp_Peq_1 = (Word)1;
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Peq['A'] = (Word)0;
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Peq['T'] = (Word)0;
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Peq['G'] = (Word)0;
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Peq['C'] = (Word)0;
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Word Peq_A;
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Word Peq_T;
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Word Peq_C;
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Word Peq_G;
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///band_length = 2k + 1
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for (i = 0; i<band_length; i++)
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{
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Peq[pattern[i]] = Peq[pattern[i]] | tmp_Peq_1;
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tmp_Peq_1 = tmp_Peq_1 << 1;
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}
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///Peq['T'] = Peq['T'] | Peq['C'];
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Peq_A = Peq['A'];
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Peq_C = Peq['C'];
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Peq_T = Peq['T'];
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Peq_G = Peq['G'];
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memset(Peq, 0, sizeof(Word)* 256);
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Peq['A'] = Peq_A;
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Peq['C'] = Peq_C;
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Peq['T'] = Peq_T;
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Peq['G'] = Peq_G;
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Word Mask = ((Word)1 << (errthold << 1));
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Word VP = 0;
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Word VN = 0;
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Word X = 0;
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Word D0 = 0;
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Word HN = 0;
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Word HP = 0;
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i = 0;
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Word column_start;
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int err = 0;
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Word err_mask = (Word)1;
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///band_down = 2k
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///i_bd = 2k
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///int i_bd = i + band_down;
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int i_bd = (errthold << 1);
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int last_high = (errthold << 1);
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/// t_length_1 = SEQ_LENGTH - 1
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int t_length_1 = t_length - 1;
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//while(i<t_length)
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while (i<t_length_1)
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{
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///pattern[0]ÔÚPeq[2k], ¶øpattern[2k]ÔÚPeq[0]
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X = Peq[text[i]] | VN;
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D0 = ((VP + (X&VP)) ^ VP) | X;
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HN = VP&D0;
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HP = VN | ~(VP | D0);
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X = D0 >> 1;
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VN = X&HP;
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VP = HN | ~(X | HP);
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if (!(D0&err_mask))
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{
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++err;
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///¼´Ê¹È«²¿µÝ¼õ£¬Ò²¾Í¼õ2k
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if ((err - last_high)>errthold)
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{
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///fprintf(stderr, "0 ######, i: %u\n", i);
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return -1;
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}
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}
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Peq['A'] = Peq['A'] >> 1;
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Peq['C'] = Peq['C'] >> 1;
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Peq['G'] = Peq['G'] >> 1;
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Peq['T'] = Peq['T'] >> 1;
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++i;
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++i_bd;
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Peq[pattern[i_bd]] = Peq[pattern[i_bd]] | Mask;
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///Peq['T'] = Peq['T'] | Peq['C'];
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column_start = i << 3;
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matrix_bit[column_start] = D0;
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matrix_bit[column_start + 1] = VP;
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matrix_bit[column_start + 2] = VN;
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matrix_bit[column_start + 3] = HP;
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matrix_bit[column_start + 4] = HN;
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}
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X = Peq[text[i]] | VN;
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D0 = ((VP + (X&VP)) ^ VP) | X;
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HN = VP&D0;
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HP = VN | ~(VP | D0);
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X = D0 >> 1;
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VN = X&HP;
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VP = HN | ~(X | HP);
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if (!(D0&err_mask))
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{
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++err;
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if ((err - last_high)>errthold)
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return -1;
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}
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column_start = (i + 1) << 3;
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matrix_bit[column_start] = D0;
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matrix_bit[column_start + 1] = VP;
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matrix_bit[column_start + 2] = VN;
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matrix_bit[column_start + 3] = HP;
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matrix_bit[column_start + 4] = HN;
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////fprintf(stderr, "sucess(2)\n");
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/// last_high = 2k
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/// site = (SEQ_LENGTH + 2k) - 2k -1
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/// site = SEQ_LENGTH - 1
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///int site = p_length - last_high - 1;
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int site = t_length - 1;
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int return_site = -1;
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if ((err <= errthold) && (err<=*return_err))
|
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{
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*return_err = err;
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return_site = site;
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}
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int i_last = i;
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i = 0;
|
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|
||||
|
||||
|
||||
|
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while (i<errthold)
|
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{
|
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err = err + ((VP >> i)&(Word)1);
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err = err - ((VN >> i)&(Word)1);
|
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++i;
|
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|
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if ((err <= errthold) && (err <= *return_err))
|
||||
{
|
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*return_err = err;
|
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return_site = site + i;
|
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}
|
||||
}
|
||||
|
||||
|
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unsigned int ungap_err;
|
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ungap_err = err;
|
||||
|
||||
|
||||
while (i<last_high)
|
||||
{
|
||||
err = err + ((VP >> i)&(Word)1);
|
||||
err = err - ((VN >> i)&(Word)1);
|
||||
++i;
|
||||
|
||||
if ((err <= errthold) && (err<=*return_err))
|
||||
{
|
||||
*return_err = err;
|
||||
return_site = site + i;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
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if ((ungap_err <= errthold) && (ungap_err == *return_err))
|
||||
{
|
||||
return_site = site + errthold;
|
||||
}
|
||||
|
||||
if ((*return_err) == (unsigned int)-1)
|
||||
{
|
||||
return return_site;
|
||||
}
|
||||
|
||||
|
||||
|
||||
///end_site是正确的
|
||||
int end_site = return_site;
|
||||
int start_site = end_site;
|
||||
///这个是各个bit-vector里面，end_site对应bit所在的位置
|
||||
int back_track_site = band_length - (p_length - end_site);
|
||||
|
||||
Word v_value, h_value, delta_value, min_value, current_value;
|
||||
Word direction, is_mismatch; ///0 is match, 1 is mismatch, 2 is up, 3 is left
|
||||
|
||||
///代表pattern到哪了，就是短的那个到哪了
|
||||
i = t_length;
|
||||
int path_length = 0;
|
||||
|
||||
///到0就结束了，后面的路径可以直接match
|
||||
current_value = *return_err;
|
||||
|
||||
|
||||
int low_bound = band_length - 1;
|
||||
|
||||
|
||||
while (i>0)
|
||||
{
|
||||
if (current_value == 0)
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
column_start = i << 3;
|
||||
|
||||
delta_value = current_value -
|
||||
((~(matrix_bit[column_start] >> back_track_site))&err_mask);
|
||||
|
||||
|
||||
if (back_track_site == 0)
|
||||
{
|
||||
///HP
|
||||
h_value = current_value - ((matrix_bit[column_start + 3] >> back_track_site)&err_mask);
|
||||
//HN
|
||||
h_value = h_value + ((matrix_bit[column_start + 4] >> back_track_site)&err_mask);
|
||||
|
||||
|
||||
min_value = delta_value;
|
||||
direction = 0;
|
||||
|
||||
if (h_value < min_value)
|
||||
{
|
||||
min_value = h_value;
|
||||
direction = 3;
|
||||
}
|
||||
|
||||
}
|
||||
else if (back_track_site == low_bound)
|
||||
{
|
||||
v_value = current_value - ((matrix_bit[column_start + 1] >> (back_track_site - 1))&err_mask);
|
||||
v_value = v_value + ((matrix_bit[column_start + 2] >> (back_track_site - 1))&err_mask);
|
||||
|
||||
min_value = delta_value;
|
||||
direction = 0;
|
||||
|
||||
if (v_value < min_value)
|
||||
{
|
||||
min_value = v_value;
|
||||
direction = 2;
|
||||
}
|
||||
|
||||
}
|
||||
else
|
||||
{
|
||||
|
||||
h_value = current_value - ((matrix_bit[column_start + 3] >> back_track_site)&(Word)1);
|
||||
|
||||
|
||||
h_value = h_value + ((matrix_bit[column_start + 4] >> back_track_site)&(Word)1);
|
||||
|
||||
|
||||
v_value = current_value - ((matrix_bit[column_start + 1] >> (back_track_site - 1))&err_mask);
|
||||
v_value = v_value + ((matrix_bit[column_start + 2] >> (back_track_site - 1))&err_mask);
|
||||
|
||||
|
||||
min_value = delta_value;
|
||||
direction = 0;
|
||||
|
||||
if (v_value < min_value)
|
||||
{
|
||||
min_value = v_value;
|
||||
direction = 2;
|
||||
}
|
||||
|
||||
|
||||
if (h_value < min_value)
|
||||
{
|
||||
min_value = h_value;
|
||||
direction = 3;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
if (direction == 0)
|
||||
{
|
||||
|
||||
if (delta_value != current_value)
|
||||
{
|
||||
direction = 1;
|
||||
}
|
||||
|
||||
i--;
|
||||
|
||||
start_site--;
|
||||
|
||||
}
|
||||
if (direction == 2)///ru guo xiang shang yi dong, bing bu huan lie
|
||||
{
|
||||
back_track_site--;
|
||||
start_site--;
|
||||
}
|
||||
else if (direction == 3)///ru guo xiang zuo yi dong
|
||||
{
|
||||
i--;
|
||||
back_track_site++;
|
||||
}
|
||||
|
||||
|
||||
path[path_length++] = direction;
|
||||
|
||||
|
||||
current_value = min_value;
|
||||
|
||||
}
|
||||
|
||||
|
||||
if (i > 0)
|
||||
{
|
||||
memset(path + path_length, 0, i);
|
||||
start_site = start_site - i;
|
||||
direction = 0;
|
||||
path_length = path_length + i;
|
||||
}
|
||||
|
||||
if (direction != 3)
|
||||
{
|
||||
start_site++;
|
||||
}
|
||||
(*return_start_site) = start_site;
|
||||
(*return_path_length) = path_length;
|
||||
|
||||
|
||||
|
||||
|
||||
return return_site;
|
||||
|
||||
}
|
||||
|
||||
inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *pattern3, char *pattern4, int p_length, char *text, int t_length,
|
||||
int* return_sites, unsigned int* return_sites_error, unsigned short errthold, __m128i* Peq_SSE)
|
||||
|
||||
|
||||
Reference in New Issue
Block a user