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save bfore multiple overlaps

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chhylp123
2020-08-23 08:46:33 -04:00
parent 90d3cb69b9
commit 03cf0d475c
15 changed files with 1120 additions and 131 deletions
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Process_Read.cpp
+54
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@@ -46,6 +46,7 @@ void destory_All_reads(All_reads* r)
if (r->read_sperate[i]) free(r->read_sperate[i]);
if (r->paf && r->paf[i].buffer) free(r->paf[i].buffer);
if (r->reverse_paf && r->reverse_paf[i].buffer) free(r->reverse_paf[i].buffer);
///if (r->pb_regions) kv_destroy(r->pb_regions[i].a);
}
free(r->paf);
free(r->reverse_paf);
@@ -55,6 +56,7 @@ void destory_All_reads(All_reads* r)
free(r->name_index);
free(r->read_length);
free(r->trio_flag);
///if (r->pb_regions) free(r->pb_regions);
}
void write_All_reads(All_reads* r, char* read_file_name)
@@ -192,6 +194,7 @@ int load_All_reads(All_reads* r, char* read_file_name)
r->second_round_cigar[i].lost_base_length = r->cigars[i].lost_base_length = 0;
r->second_round_cigar[i].lost_base = r->cigars[i].lost_base = NULL;
}
///r->pb_regions = NULL;
free(index_name);
fclose(fp);
@@ -263,6 +266,8 @@ void malloc_All_reads(All_reads* r)
r->second_round_cigar = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
r->paf = (ma_hit_t_alloc*)malloc(sizeof(ma_hit_t_alloc)*r->total_reads);
r->reverse_paf = (ma_hit_t_alloc*)malloc(sizeof(ma_hit_t_alloc)*r->total_reads);
///r->pb_regions = (kvec_t_u64_warp*)malloc(r->total_reads*sizeof(kvec_t_u64_warp));
for (i = 0; i < (long long)r->total_reads; i++)
{
r->second_round_cigar[i].size = r->cigars[i].size = 0;
@@ -274,6 +279,7 @@ void malloc_All_reads(All_reads* r)
r->second_round_cigar[i].lost_base = r->cigars[i].lost_base = NULL;
init_ma_hit_t_alloc(&(r->paf[i]));
init_ma_hit_t_alloc(&(r->reverse_paf[i]));
///kv_init(r->pb_regions[i].a);
}
r->name = (char*)malloc(sizeof(char)*r->total_name_length);
@@ -667,3 +673,51 @@ void reverse_complement(char* pattern, uint64_t length)
pattern[end] = RC_CHAR(pattern[end]);
}
}
void init_Debug_reads(Debug_reads* x, const char* file)
{
int nameLen, i, bufLen = 1000;
if((uint64_t)(bufLen) < strlen(file) + 50) bufLen = strlen(file) + 50;
char* Name_Buffer = (char*)malloc(sizeof(char)*bufLen);
fprintf(stderr, "Queried debugging reads at: %s\n", file);
x->fp = fopen(file,"r");
x->query_num = 0;
while(fgets(Name_Buffer, bufLen, x->fp))
{
x->query_num++;
}
x->read_name = (char**)malloc(sizeof(char*)*x->query_num);
fseek(x->fp, 0, SEEK_SET);
i = 0;
while(fgets(Name_Buffer, bufLen, x->fp))
{
nameLen = strlen(Name_Buffer) - 1;
x->read_name[i] = (char*)malloc(sizeof(char)*(nameLen+1));
memcpy(x->read_name[i], Name_Buffer, sizeof(char)*nameLen);
x->read_name[i][nameLen] = '\0';
i++;
}
fclose(x->fp);
sprintf(Name_Buffer, "%s.debug.stdout", file);
x->fp = fopen(Name_Buffer,"w");
fprintf(stderr, "Print debugging information to: %s\n", Name_Buffer);
free(Name_Buffer);
}
void destory_Debug_reads(Debug_reads* x)
{
uint64_t i;
for (i = 0; i < x->query_num; i++)
{
free(x->read_name[i]);
}
free(x->read_name);
fclose(x->fp);
}