mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-01 14:18:12 +08:00
resure alignment
This commit is contained in:
Haoyu Cheng
+6
-24
@@ -773,8 +773,8 @@ void* Overlap_calculate_heap_merge(void* arg)
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/************需要注释掉**********/
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// debug_overlap = debug_overlap + list_length;
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/************需要注释掉**********/
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///append_k_mer_pos_list_alloc(&array_list, list, list_length, end_pos, 0);
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append_k_mer_pos_list_alloc_prefilter(&array_list, list, list_length, end_pos, 0, &g_read, &R_INF, &correct);
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append_k_mer_pos_list_alloc(&array_list, list, list_length, end_pos, 0);
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///append_k_mer_pos_list_alloc_prefilter(&array_list, list, list_length, end_pos, 0, &g_read, &R_INF, &correct);
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}
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///merge_Candidates_list(&l, list, list_length, end_pos, 0);
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///merge_Candidates_list_version(&debug_l, list, list_length, end_pos, 0);
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@@ -833,8 +833,8 @@ void* Overlap_calculate_heap_merge(void* arg)
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/************需要注释掉**********/
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// debug_overlap = debug_overlap + list_length;
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/************需要注释掉**********/
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///append_k_mer_pos_list_alloc(&array_list, list, list_length, end_pos, 1);
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append_k_mer_pos_list_alloc_prefilter(&array_list, list, list_length, end_pos, 1, &g_read, &R_INF, &correct);
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append_k_mer_pos_list_alloc(&array_list, list, list_length, end_pos, 1);
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///append_k_mer_pos_list_alloc_prefilter(&array_list, list, list_length, end_pos, 1, &g_read, &R_INF, &correct);
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}
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///merge_Candidates_list(&l, list, list_length, end_pos, 1);
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//merge_Candidates_list_version(&debug_l, list, list_length, end_pos, 1);
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@@ -879,24 +879,6 @@ void* Overlap_calculate_heap_merge(void* arg)
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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 * 0.9 <= 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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matched_overlap_0++;
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}
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else
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{
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matched_overlap_1++;
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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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@@ -994,8 +976,8 @@ void* Overlap_calculate_heap_merge(void* arg)
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//destory_Candidates_list(&debug_l);
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destory_Heap(&heap);
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///destory_k_mer_pos_list_alloc(&array_list);
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destory_k_mer_pos_list_alloc_prefilter(&array_list);
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destory_k_mer_pos_list_alloc(&array_list);
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///destory_k_mer_pos_list_alloc_prefilter(&array_list);
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destory_Graph(&POA_Graph);
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destory_UC_Read(&g_read);
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+850
-83
File diff suppressed because it is too large
Load Diff
@@ -4,9 +4,8 @@
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#include "Hash_Table.h"
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#include "Levenshtein_distance.h"
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#define WINDOW 350
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#define THRESHOLD 15
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#define GROUP_SIZE 4
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#define MAX(x, y) ((x >= y)?x:y)
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#define MIN(x, y) ((x <= y)?x:y)
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@@ -22,6 +21,9 @@ typedef struct
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uint64_t start_i;
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char overlap_region[WINDOW + THRESHOLD*2 + 10];
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char overlap_region_group[GROUP_SIZE][WINDOW + THRESHOLD*2 + 10];
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char path[WINDOW + THRESHOLD*2 + 10];
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int path_length;
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Word matrix_bit[((WINDOW + 10)<<3)];
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__m128i Peq_SSE[256];
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} Correct_dumy;
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+39
-1
@@ -212,15 +212,29 @@ void init_overlap_region_alloc(overlap_region_alloc* list)
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{
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list->size = 1000;
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list->length = 0;
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list->list = (overlap_region*)malloc(sizeof(overlap_region)*list->size);
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///list->list = (overlap_region*)malloc(sizeof(overlap_region)*list->size);
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list->list = (overlap_region*)calloc(list->size, sizeof(overlap_region));
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}
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void clear_overlap_region_alloc(overlap_region_alloc* list)
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{
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list->length = 0;
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int i = 0;
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for (i = 0; i < list->size; i++)
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{
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list->list[i].w_list_length = 0;
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}
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}
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void destory_overlap_region_alloc(overlap_region_alloc* list)
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{
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int i = 0;
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for (i = 0; i < list->size; i++)
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{
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if (list->list[i].w_list_size != 0)
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{
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free(list->list[i].w_list);
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}
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}
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free(list->list);
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}
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@@ -235,6 +249,8 @@ void append_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp
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{
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list->size = list->size * 2;
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list->list = (overlap_region*)realloc(list->list, sizeof(overlap_region)*list->size);
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///新分配空间要初始化
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memset(list->list + (list->size/2), 0, sizeof(overlap_region)*(list->size/2));
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}
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if (list->length!=0 &&
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@@ -641,6 +657,28 @@ uint64_t readID, uint64_t readLength, All_reads* R_INF)
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void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error)
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{
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long long length = region->x_pos_e - region->x_pos_s + 1;
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long long num_windows = length / WINDOW + 2;
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///w_list_length会在clear_overlap_region_alloc中定时清空
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if (num_windows > region->w_list_size)
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{
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region->w_list_size = num_windows;
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region->w_list = (window_list*)realloc(region->w_list, region->w_list_size*sizeof(window_list));
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}
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region->w_list[region->w_list_length].x_start = x_start;
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region->w_list[region->w_list_length].x_end = x_end;
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region->w_list[region->w_list_length].y_start = y_start;
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region->w_list[region->w_list_length].y_end = y_end;
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region->w_list[region->w_list_length].error = error;
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region->w_list[region->w_list_length].cigar.length = -1;
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region->w_list_length++;
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}
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+33
-2
@@ -13,6 +13,14 @@ typedef khash_t(POS64) Pos_Table;
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#define MAX_SUFFIX_BITS 64
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#define MODE_VALUE 101
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///#define WINDOW 350
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///#define THRESHOLD 14
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#define WINDOW 375
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#define THRESHOLD 15
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#define THRESHOLD_RATE 0.04
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#define GROUP_SIZE 4
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///最长是10M10D10M10D10M这种
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#define CIGAR_MAX_LENGTH THRESHOLD*2+2
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typedef struct
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{
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@@ -53,6 +61,26 @@ typedef struct
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uint64_t length;
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} k_mer_pos_list_alloc;
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typedef struct
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{
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int C_L[CIGAR_MAX_LENGTH];
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char C_C[CIGAR_MAX_LENGTH];
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int length;
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} CIGAR;
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typedef struct
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{
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uint64_t x_start;
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uint64_t x_end;
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int y_end;
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int y_start;
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///int y_pre_start;
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///error小于等于0都要重新算
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int error;
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CIGAR cigar;
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} window_list;
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typedef struct
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{
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uint64_t x_id;
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@@ -67,6 +95,10 @@ typedef struct
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uint64_t shared_seed;
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uint64_t align_length;
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window_list* w_list;
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uint64_t w_list_size;
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uint64_t w_list_length;
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} overlap_region;
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@@ -406,8 +438,7 @@ void destory_overlap_region_alloc(overlap_region_alloc* list);
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void append_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp, All_reads* R_INF);
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void calculate_overlap_region(Candidates_list* candidates, overlap_region_alloc* overlap_list,
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uint64_t readID, uint64_t readLength, All_reads* R_INF);
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void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error);
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+90
-148
@@ -172,6 +172,10 @@ inline int Reserve_Banded_BPM
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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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///p_length大部分情况下应该是t_length + 2 * errthold，这是i要小于last_high = 2 * errthold
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///也就是p_length - t_length
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///那么当p_length < t_length + 2 * errthold, available_i也应该是这个值
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int available_i = p_length - t_length;
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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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@@ -181,9 +185,7 @@ inline int Reserve_Banded_BPM
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i = 0;
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while (i<errthold)
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while (i < available_i)
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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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@@ -196,45 +198,85 @@ inline int Reserve_Banded_BPM
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}
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}
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unsigned int ungap_err;
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ungap_err = err;
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while (i<last_high)
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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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if ((err <= errthold) && (err<=*return_err))
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{
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*return_err = err;
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return_site = site + i;
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}
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}
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if ((ungap_err <= errthold) && (ungap_err == *return_err))
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{
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return_site = site + errthold;
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}
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return return_site;
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}
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inline int try_cigar(char *pattern, int p_length,
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char *text, int t_length, int end_site, char* path,
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int error,
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int* return_start_site,
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int* return_path_length)
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{
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int i = 0;
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int tmp_err = 0;
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///y上的起始位置
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int start_site = end_site - t_length + 1;
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if (start_site >= 0)
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{
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for (i = 0; i < t_length; i++)
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{
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///path[i] = 0;
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///path倒着存
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path[t_length - i - 1] = 0;
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if (text[i] != pattern[i + start_site])
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{
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path[t_length - i - 1] = 1;
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tmp_err++;
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if (tmp_err > error)
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{
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return 0;
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}
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}
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}
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if (tmp_err == error)
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{
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(*return_path_length) = t_length;
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(*return_start_site) = start_site;
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return 6;
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}
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}
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return 0;
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}
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///p_length有可能不够，但是t_length总是够的
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///就是p_length有可能小于t_length + 2 * errthold
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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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unsigned int* return_err, int* return_start_site, int* return_path_length, Word* matrix_bit, char* path,
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int old_error, int old_end_site)
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{
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if (old_error != -1 && old_end_site != -1)
|
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{
|
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if (old_error == 0)
|
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{
|
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///fprintf(stderr, "0 error\n");
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(*return_err) = old_error;
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(*return_start_site) = old_end_site - t_length + 1;
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return old_end_site;
|
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}
|
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|
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if (try_cigar(pattern, p_length, text, t_length, old_end_site, path,
|
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old_error, return_start_site, return_path_length))
|
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{
|
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///fprintf(stderr, "no gap error\n");
|
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(*return_err) = old_error;
|
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return old_end_site;
|
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}
|
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|
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}
|
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|
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(*return_err) = (unsigned int)-1;
|
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|
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Word Peq[256];
|
||||
@@ -330,10 +372,8 @@ inline int Reserve_Banded_BPM_PATH
|
||||
{
|
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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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///fprintf(stderr, "0 ######, i: %u\n", i);
|
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return -1;
|
||||
}
|
||||
|
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@@ -396,6 +436,10 @@ inline int Reserve_Banded_BPM_PATH
|
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///int site = p_length - last_high - 1;
|
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int site = t_length - 1;
|
||||
int return_site = -1;
|
||||
///p_length大部分情况下应该是t_length + 2 * errthold，这是i要小于last_high = 2 * errthold
|
||||
///也就是p_length - t_length
|
||||
///那么当p_length < t_length + 2 * errthold, available_i也应该是这个值
|
||||
int available_i = p_length - t_length;
|
||||
if ((err <= errthold) && (err<=*return_err))
|
||||
{
|
||||
*return_err = err;
|
||||
@@ -404,10 +448,7 @@ inline int Reserve_Banded_BPM_PATH
|
||||
int i_last = i;
|
||||
i = 0;
|
||||
|
||||
|
||||
|
||||
|
||||
while (i<errthold)
|
||||
while (i < available_i)
|
||||
{
|
||||
err = err + ((VP >> i)&(Word)1);
|
||||
err = err - ((VN >> i)&(Word)1);
|
||||
@@ -421,40 +462,15 @@ inline int Reserve_Banded_BPM_PATH
|
||||
}
|
||||
|
||||
|
||||
unsigned int ungap_err;
|
||||
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;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
if ((ungap_err <= errthold) && (ungap_err == *return_err))
|
||||
{
|
||||
return_site = site + errthold;
|
||||
}
|
||||
|
||||
if ((*return_err) == (unsigned int)-1)
|
||||
{
|
||||
return return_site;
|
||||
}
|
||||
|
||||
|
||||
|
||||
////注意，这里p_length要矫正啊啊
|
||||
///不矫正会出错
|
||||
///因为p_length有可能不够
|
||||
p_length = t_length + 2 * errthold;
|
||||
///end_site是正确的
|
||||
int end_site = return_site;
|
||||
int start_site = end_site;
|
||||
@@ -608,6 +624,8 @@ inline int Reserve_Banded_BPM_PATH
|
||||
|
||||
}
|
||||
|
||||
|
||||
////这个p_length四个是一样的
|
||||
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)
|
||||
|
||||
@@ -829,8 +847,12 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
|
||||
i = 0;
|
||||
|
||||
|
||||
///p_length大部分情况下应该是t_length + 2 * errthold，这是i要小于last_high = 2 * errthold
|
||||
///也就是p_length - t_length
|
||||
///那么当p_length < t_length + 2 * errthold, available_i也应该是这个值
|
||||
int available_i = p_length - t_length;
|
||||
|
||||
while (i<errthold)
|
||||
while (i < available_i)
|
||||
{
|
||||
///err = err + ((VP >> i)&(Word_32)1);
|
||||
tmp_process = _mm_srli_epi32(VP, i);
|
||||
@@ -871,87 +893,7 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
unsigned int ungap_err1;
|
||||
unsigned int ungap_err2;
|
||||
unsigned int ungap_err3;
|
||||
unsigned int ungap_err4;
|
||||
ungap_err1 = err1;
|
||||
ungap_err2 = err2;
|
||||
ungap_err3 = err3;
|
||||
ungap_err4 = err4;
|
||||
|
||||
|
||||
|
||||
|
||||
while (i<last_high)
|
||||
{
|
||||
///err = err + ((VP >> i)&(Word_32)1);
|
||||
tmp_process = _mm_srli_epi32(VP, i);
|
||||
tmp_process = _mm_and_si128(tmp_process, err_mask);
|
||||
Err_4 = _mm_add_epi32(Err_4, tmp_process);
|
||||
|
||||
///err = err - ((VN >> i)&(Word_32)1);
|
||||
tmp_process1 = _mm_srli_epi32(VN, i);
|
||||
tmp_process1 = _mm_and_si128(tmp_process1, err_mask);
|
||||
Err_4 = _mm_sub_epi32(Err_4, tmp_process1);
|
||||
++i;
|
||||
|
||||
err1 = _mm_extract_epi32(Err_4, 0);
|
||||
err2 = _mm_extract_epi32(Err_4, 1);
|
||||
err3 = _mm_extract_epi32(Err_4, 2);
|
||||
err4 = _mm_extract_epi32(Err_4, 3);
|
||||
|
||||
|
||||
if ((err1 <= errthold) && (err1 <= return_sites_error[0]))
|
||||
{
|
||||
return_sites[0] = site + i;
|
||||
return_sites_error[0] = err1;
|
||||
}
|
||||
if ((err2 <= errthold) && (err2 <= return_sites_error[1]))
|
||||
{
|
||||
return_sites[1] = site + i;
|
||||
return_sites_error[1] = err2;
|
||||
}
|
||||
if ((err3 <= errthold) && (err3 <= return_sites_error[2]))
|
||||
{
|
||||
return_sites[2] = site + i;
|
||||
return_sites_error[2] = err3;
|
||||
}
|
||||
if ((err4 <= errthold) && (err4 <= return_sites_error[3]))
|
||||
{
|
||||
return_sites[3] = site + i;
|
||||
return_sites_error[3] = err4;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if ((ungap_err1 <= errthold) && ungap_err1 == return_sites_error[0])
|
||||
{
|
||||
return_sites[0] = site + errthold;
|
||||
}
|
||||
|
||||
|
||||
if ((ungap_err2 <= errthold) && ungap_err2 == return_sites_error[1])
|
||||
{
|
||||
return_sites[1] = site + errthold;
|
||||
}
|
||||
|
||||
|
||||
if ((ungap_err3 <= errthold) && ungap_err3 == return_sites_error[2])
|
||||
{
|
||||
return_sites[2] = site + errthold;
|
||||
}
|
||||
|
||||
|
||||
if ((ungap_err4 <= errthold) && ungap_err4 == return_sites_error[3])
|
||||
{
|
||||
return_sites[3] = site + errthold;
|
||||
}
|
||||
|
||||
return 1;
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@@ -138,9 +138,11 @@ void debug_edit_distance()
|
||||
char* x = "TTCCATACGATTCCATTCAATTCGAGACCATTCTATTCCTGTCCATTCCTTGTGGTTCGATTCCATTTCACTCTAGTCCATTCCATTCCATTCAATTCCATTCGACTCTATTCCGTTCCACTCAATTCCATTCCATTCGATTCCATTTTTTTCGAGAACCTTCCATTACACTCCCTTCCATTCCAGTGCATTCCATTCCAGTCTCTTCAGTTCGATTCCATTCCATTCGTTTCGATTCCTTTCCATTCCAGCCCATTCCATTCCATTCCATTCCTTTCCTTTCCGTTTCATTAGATTCCATTGCATTCGATTCCATTCAAATCAATTCCGTTCTATTCAATTTGATTCAT";
|
||||
char* y = "CCATACGATTCCATTCAATTCGAGACCATTCTATTCCTGTCCATTCCTTGTGGTTCGATTCCATTTCACTCTAGTCCATTCCATTCCATTCAATTCCATTCGACTCTATTCCGTTCCATTCAATTCCATTCCATTCGATTCCATTTTTTTCGAGAACCTTCCATTACACTCCCTTCCATTCCAGTGCATTCCATTCCAGTCTCTTCACTTCGATTCCATTCCATTCGTTTCGATTCCTTTCCATTCCAGCCCATTCCATTCCATTCCATTCCTTTCCTTTCCGTTTCATTAGATTCCATTGCATTCCATTCCATTCAATTCAATTCCGTGCTATTCAATTTGATTCATTTCCATTTAATTCCATTCCATTAGATTCCATT";
|
||||
**/
|
||||
unsigned short toold = 7;
|
||||
char* x = "TTCCATACGATTCCATTCAATTCGAGACCATTCTATTCCT";
|
||||
char* y = "CCATACGATTCCATTCAATTCGAGACCATTCTATTCCTGTCCATTCCTTGTGGT";
|
||||
unsigned short toold = 15;
|
||||
char* x
|
||||
= "GAAAGAGAATCAAATGGAATTGAATCGAATGGAATCGAATGGATTGGAAAGGAATAGAATGGAATGGAATGGAATTGACTCAAATGGAATGGACTAGAATGGAATGGATTCGAATGGAAGGCAAAGGAATGGAATCTATCGGAATGGACTGTAATGGAATGGAATGGAAGGGATTGGAATGGATTCGAATGTAATGGACTGCAATAGAAAGGATTCGAATGGAATGAAAAAGAATTGAATGGAATAGAACAGAATGGAATCAAATCGAAGGAAATGGAATGGAATAGAAAGGAATGGAATGAAATGGAATGGAAAGGATTCGAATGGAATGCAATCGAATGGAATGGAATCGAACGGAATGGAATAAAATGGAAG";
|
||||
char* y =
|
||||
"GAAAGAGAATCAAATGGAATTGAATCGAATGGAATCGAATGGATTGGAAAGGAATAGAATGGAATGGAATGGAATGGACTCAAATGGAATGTACTAGAATGGAATGGATTCGAATGGAAGGCAAAGGAATGGAATCTATTGGAATGGACTGTAATGGAATGGAATGGAAGGGATTGGAATGGACTCGAATGGAATGGACTGCAATAGAAAGGATTCGAATGGAATGAAAAAGAATTGAATGGAATAGAACAGAATGGAATCAAATCGAATGAAATGGAATGGAATAGAAAGGAATGGAATGAAATGGAATGGAAAGGATTCGAATGGAATGCAATCGAATGGAATGGAATCGAACGGAATGGAATAAATTTTCTG";
|
||||
fprintf(stderr, "x_length: %u\n", strlen(x));
|
||||
fprintf(stderr, "y_length: %u\n", strlen(y));
|
||||
|
||||
@@ -204,6 +206,8 @@ int main(int argc, char *argv[])
|
||||
|
||||
return 1;
|
||||
**/
|
||||
|
||||
|
||||
|
||||
|
||||
fprintf(stdout, "k-mer length: %d\n",k_mer_length);
|
||||
|
||||
Reference in New Issue
Block a user