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for hifiasm 3.0

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This commit is contained in:
chhylp123
2020-03-22 16:54:32 -04:00
parent 6ae51c84f6
commit c72d419711
16 changed files with 38378 additions and 654 deletions
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66
Process_Read.cpp
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@@ -59,6 +59,7 @@ void init_All_reads(All_reads* r)
r->name = NULL;
r->total_name_length = 0;
r->total_reads = 0;
r->trio_flag = NULL;
}
void destory_All_reads(All_reads* r)
@@ -77,6 +78,7 @@ void destory_All_reads(All_reads* r)
free(r->name);
free(r->name_index);
free(r->read_length);
free(r->trio_flag);
}
@@ -123,6 +125,7 @@ void write_All_reads(All_reads* r, char* read_file_name)
fwrite(r->name, sizeof(char), r->total_name_length, fp);
fwrite(r->name_index, sizeof(uint64_t), r->name_index_size, fp);
fwrite(r->trio_flag, sizeof(uint8_t), r->total_reads, fp);
free(index_name);
fflush(fp);
fclose(fp);
@@ -201,6 +204,10 @@ int load_All_reads(All_reads* r, char* read_file_name)
r->name_index = (uint64_t*)malloc(sizeof(uint64_t)*r->name_index_size);
f_flag += fread(r->name_index, sizeof(uint64_t), r->name_index_size, fp);
/****************************may have bugs********************************/
r->trio_flag = (uint8_t*)malloc(sizeof(uint8_t)*r->total_reads);
f_flag += fread(r->trio_flag, sizeof(uint8_t), r->total_reads, fp);
/****************************may have bugs********************************/
r->cigars = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
r->second_round_cigar = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
@@ -279,7 +286,8 @@ void malloc_All_reads(All_reads* r)
r->name = (char*)malloc(sizeof(char)*r->total_name_length);
r->N_site = (uint64_t**)calloc(r->total_reads, sizeof(uint64_t*));
r->trio_flag = (uint8_t*)malloc(r->total_reads*sizeof(uint8_t));
memset(r->trio_flag, AMBIGU, r->total_reads*sizeof(uint8_t));
}
void destory_UC_Read(UC_Read* r)
@@ -1065,3 +1073,59 @@ void reverse_complement(char* pattern, uint64_t length)
}
typedef struct {
char* tmp;
long long tmpSize;
char* dest;
long long destSize;
FILE* fp;
} LineReader;
int get_single_line(LineReader* line)
{
long long currentLen = 0, getLen = 0;
line->tmp[0] = '\0';
while (fgets(line->tmp, line->tmpSize, line->fp) != NULL)
{
getLen = strlen(line->tmp);
if(getLen + currentLen >= line->destSize)
{
line->destSize = getLen + currentLen + 1;
line->dest = (char*)realloc(line->dest, line->destSize);
}
memcpy(line->dest + currentLen, line->tmp, getLen+1);
currentLen = currentLen + getLen;
if(currentLen > 0 && line->dest[currentLen - 1] == '\n')
{
return 1;
}
}
if(currentLen > 0)
{
return 1;
}
else
{
return 0;
}
}
void get_trio_info(char* input, uint8_t* pm)
{
uint32_t i;
(*pm) = AMBIGU;
for (i = 0; input[i] != '\0'; i++)
{
if(input[i] == '\t')
{
break;
}
}
input[i] = '\0';
i++;
if(input[i] == 'p') (*pm) = FATHER;
if(input[i] == 'm') (*pm) = MOTHER;
}