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chhylp123
2024-11-12 23:53:29 -05:00
parent 6de4e14782
commit 80fa5ed436
11 changed files with 1211 additions and 135 deletions
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38
Assembly.cpp
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@@ -904,6 +904,29 @@ void Output_corrected_reads()
fclose(output_file);
}
void Output_corrected_fastq()
{
long long i; uint64_t k;
UC_Read g_read; asg8_v dv;
init_UC_Read(&g_read); kv_init(dv);
char* gfa_name = (char*)malloc(strlen(asm_opt.output_file_name)+35);
sprintf(gfa_name, "%s.ec.fq", asm_opt.output_file_name);
FILE* fp = fopen(gfa_name, "w");
free(gfa_name);
for (i = 0; i < (long long)R_INF.total_reads; i++) {
recover_UC_Read(&g_read, &R_INF, i);
fprintf(fp, "@%.*s\n", (int32_t)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
fprintf(fp, "%.*s\n", (int32_t)g_read.length, g_read.seq);
fprintf(fp, "+\n");
retrive_bqual(&dv, NULL, i, -1, -1, 0, sc_bn);
for (k = 0; k < dv.n; k++) fprintf(fp, "%c", (char)(sc_tb[dv.a[k]] + 33 - 1));
fprintf(fp, "\n");
}
destory_UC_Read(&g_read); kv_destroy(dv);
fclose(fp);
}
void debug_print_pob_regions()
{
uint64_t i, total = 0;
@@ -992,9 +1015,12 @@ void ha_ec(int64_t round, int num_pround, int des_idx, uint64_t *tot_b, uint64_t
if (r_out) write_pt_index(ha_flt_tab, ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name);
// Output_corrected_fastq();
cal_ec_r(asm_opt.thread_num, round, num_pround, R_INF.total_reads, (round == (asm_opt.number_of_round-1))?1:0, tot_b, tot_e);
// exit(1);
// exit(1);
// if (r_out) write_pt_index(ha_flt_tab, ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name);
if(des_idx) {
@@ -2014,7 +2040,10 @@ int ha_assemble(void)
ha_extract_print_list(&R_INF, asm_opt.extract_iter, asm_opt.extract_list);
exit(0);
}
if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();
if (asm_opt.flag & HA_F_WRITE_EC) {
if(asm_opt.is_sc) Output_corrected_fastq();
else Output_corrected_reads();
}
if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
if (asm_opt.het_cov == -1024) hap_recalculate_peaks(asm_opt.output_file_name), ovlp_loaded = 2;
}
@@ -2042,7 +2071,10 @@ int ha_assemble(void)
// asm_opt.num_bases, asm_opt.num_corrected_bases, asm_opt.num_recorrected_bases);
// fprintf(stderr, "[M::%s] size of buffer: %.3fGB\n", __func__, asm_opt.mem_buf / 1073741824.0);
}
if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();
if (asm_opt.flag & HA_F_WRITE_EC) {
if(asm_opt.is_sc) Output_corrected_fastq();
else Output_corrected_reads();
}
// overlap between corrected reads
ha_opt_reset_to_round(&asm_opt, asm_opt.number_of_round);
// ha_overlap_final();