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update k-mer peaks

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chhylp123
2020-07-07 13:20:25 -04:00
parent 2e56ef7db5
commit a25c37ed89
9 changed files with 106 additions and 28 deletions
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34
Process_Read.cpp
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@@ -98,6 +98,9 @@ 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);
fwrite(&(asm_opt.hom_cov), sizeof(asm_opt.hom_cov), 1, fp);
fwrite(&(asm_opt.het_cov), sizeof(asm_opt.het_cov), 1, fp);
free(index_name);
fflush(fp);
fclose(fp);
@@ -173,6 +176,8 @@ int load_All_reads(All_reads* r, char* read_file_name)
/****************************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);
f_flag += fread(&(asm_opt.hom_cov), sizeof(asm_opt.hom_cov), 1, fp);
f_flag += fread(&(asm_opt.het_cov), sizeof(asm_opt.het_cov), 1, fp);
/****************************may have bugs********************************/
r->cigars = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
@@ -195,6 +200,35 @@ int load_All_reads(All_reads* r, char* read_file_name)
return 1;
}
int destory_read_bin(All_reads* r)
{
uint64_t i = 0;
for (i = 0; i < r->total_reads; i++)
{
if (r->N_site[i]) free(r->N_site[i]);
if (r->read_sperate[i]) free(r->read_sperate[i]);
if (r->cigars[i].record) free(r->cigars[i].record);
if (r->cigars[i].lost_base) free(r->cigars[i].lost_base);
if (r->second_round_cigar[i].record) free(r->second_round_cigar[i].record);
if (r->second_round_cigar[i].lost_base) free(r->second_round_cigar[i].lost_base);
}
free(r->N_site);
free(r->read_length);
free(r->read_size);
free(r->read_sperate);
free(r->name);
free(r->name_index);
free(r->trio_flag);
free(r->cigars);
free(r->second_round_cigar);
return 1;
}
void ha_insert_read_len(All_reads *r, int read_len, int name_len)
{
r->total_reads++;