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changed the output file names

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This commit is contained in:
Heng Li
2019-12-30 12:01:54 -05:00
parent 30eddefc57
commit 3a61b1b0b0
4 changed files with 102 additions and 78 deletions
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Overlaps.cpp
+42 -52
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@@ -7041,29 +7041,34 @@ const long long n_read)
return 0;
}
void ma_ug_print(const ma_ug_t *ug, All_reads *RNF, const ma_sub_t *coverage_cut, FILE *fp)
void ma_ug_print2(const ma_ug_t *ug, All_reads *RNF, const ma_sub_t *coverage_cut, int print_seq, FILE *fp)
{
uint32_t i, j, l;
char name[32];
for (i = 0; i < ug->u.n; ++i) { // the Segment lines in GFA
ma_utg_t *p = &ug->u.a[i];
sprintf(name, "utg%.6d%c", i + 1, "lc"[p->circ]);
fprintf(fp, "S\t%s\t%s\tLN:i:%d\n", name, p->s? p->s : "*", p->len);
if (print_seq) fprintf(fp, "S\t%s\t%s\tLN:i:%d\n", name, p->s? p->s : "*", p->len);
else fprintf(fp, "S\t%s\t*\tLN:i:%d\n", name, p->len);
for (j = l = 0; j < p->n; l += (uint32_t)p->a[j++]) {
uint32_t x = p->a[j]>>33;
fprintf(fp, "a\t%s\t%d\t%.*s(%u):%d-%d\t%c\t%d\n", name, l,
(int)Get_NAME_LENGTH((*RNF), x), Get_NAME((*RNF), x), x,
coverage_cut[x].s + 1, coverage_cut[x].e, "+-"[p->a[j]>>32&1], (uint32_t)p->a[j]);
fprintf(fp, "A\t%s\t%d\t%c\t%.*s\t%d\t%d\tid:i:%d\n", name, l, "+-"[p->a[j]>>32&1], (int)Get_NAME_LENGTH((*RNF), x),
Get_NAME((*RNF), x), coverage_cut[x].s, coverage_cut[x].e, x);
}
}
for (i = 0; i < ug->g->n_arc; ++i) { // the Link lines in GFA
uint32_t u = ug->g->arc[i].ul>>32, v = ug->g->arc[i].v;
fprintf(fp, "L\tutg%.6d%c\t%c\tutg%.6d%c\t%c\t%dM\tSD:i:%d\n", (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
fprintf(fp, "L\tutg%.6d%c\t%c\tutg%.6d%c\t%c\t%dM\tL1:i:%d\n", (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
(v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], ug->g->arc[i].ol, asg_arc_len(ug->g->arc[i]));
}
}
void ma_ug_print(const ma_ug_t *ug, All_reads *RNF, const ma_sub_t *coverage_cut, FILE *fp)
{
ma_ug_print2(ug, RNF, coverage_cut, 1, fp);
}
int asg_cut_internal(asg_t *g, int max_ext)
{
asg64_v a = {0,0,0};
@@ -7310,18 +7315,7 @@ void ma_sg_print(const asg_t *g, const All_reads *RNF, const ma_sub_t *sub, FILE
void ma_ug_print_simple(const ma_ug_t *ug, All_reads *RNF, const ma_sub_t *coverage_cut, FILE *fp)
{
uint32_t i;
char name[32];
for (i = 0; i < ug->u.n; ++i) { // the Segment lines in GFA
ma_utg_t *p = &ug->u.a[i];
sprintf(name, "utg%.6d%c", i + 1, "lc"[p->circ]);
fprintf(fp, "S\t%s\t%s\tLN:i:%d\n", name, "*", p->len);
}
for (i = 0; i < ug->g->n_arc; ++i) { // the Link lines in GFA
uint32_t u = ug->g->arc[i].ul>>32, v = ug->g->arc[i].v;
fprintf(fp, "L\tutg%.6d%c\t%c\tutg%.6d%c\t%c\t%dM\tSD:i:%d\n", (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
(v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], ug->g->arc[i].ol, asg_arc_len(ug->g->arc[i]));
}
ma_ug_print2(ug, RNF, coverage_cut, 0, fp);
}
@@ -7737,16 +7731,16 @@ void output_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_na
ug = ma_ug_gen(sg);
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
fprintf(stderr, "Writing unitig GFA to disk... \n");
fprintf(stderr, "Writing raw unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.utg.gfa", output_file_name);
sprintf(gfa_name, "%s.r_utg.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
// sprintf(gfa_name, "%s.simple.gfa", output_file_name);
// output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
// fclose(output_file);
sprintf(gfa_name, "%s.r_utg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);
@@ -7887,13 +7881,13 @@ void write_all_data_to_disk(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sou
All_reads *RNF, char* output_file_name)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.gfa.aux", output_file_name);
sprintf(gfa_name, "%s.ovlp", output_file_name);
write_All_reads(RNF, gfa_name);
sprintf(gfa_name, "%s.gfa.aux.source", output_file_name);
sprintf(gfa_name, "%s.ovlp.source", output_file_name);
write_ma_hit_ts(sources, RNF->total_reads, gfa_name);
sprintf(gfa_name, "%s.gfa.aux.reverse", output_file_name);
sprintf(gfa_name, "%s.ovlp.reverse", output_file_name);
write_ma_hit_ts(reverse_sources, RNF->total_reads, gfa_name);
free(gfa_name);
@@ -7903,20 +7897,20 @@ int load_all_data_from_disk(ma_hit_t_alloc **sources, ma_hit_t_alloc **reverse_s
char* output_file_name)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.gfa.aux", output_file_name);
sprintf(gfa_name, "%s.ovlp.aux", output_file_name);
if(!load_All_reads(&R_INF, gfa_name))
{
return 0;
}
sprintf(gfa_name, "%s.gfa.aux.source", output_file_name);
sprintf(gfa_name, "%s.ovlp.source", output_file_name);
if(!load_ma_hit_ts(sources, gfa_name))
{
return 0;
}
sprintf(gfa_name, "%s.gfa.aux.reverse", output_file_name);
sprintf(gfa_name, "%s.ovlp.reverse", output_file_name);
if(!load_ma_hit_ts(reverse_sources, gfa_name))
{
return 0;
@@ -8770,17 +8764,17 @@ char* output_file_name, long long n_read, long long bubble_dist, long long tipsL
ug = ma_ug_gen_primary(sg, 0);
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
fprintf(stderr, "Writing unitig GFA to disk... \n");
fprintf(stderr, "Writing processed unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
sprintf(gfa_name, "%s.wsb.utg.gfa", output_file_name);
sprintf(gfa_name, "%s.p_utg.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
// sprintf(gfa_name, "%s.simple.no_s_bub.gfa", output_file_name);
// output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
// fclose(output_file);
sprintf(gfa_name, "%s.p_utg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);
@@ -8883,21 +8877,17 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
ug = ma_ug_gen_primary(sg, 0);
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
fprintf(stderr, "Writing unitig GFA to disk... \n");
fprintf(stderr, "Writing primary contig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
sprintf(gfa_name, "%s.ctg.gfa", output_file_name);
sprintf(gfa_name, "%s.p_ctg.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
// sprintf(gfa_name, "%s.simple.contig.gfa", output_file_name);
// output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
// fclose(output_file);
sprintf(gfa_name, "%s.p_ctg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);
@@ -8910,17 +8900,17 @@ void output_contig_graph_alternative(asg_t *sg, ma_sub_t* coverage_cut, char* ou
ug = ma_ug_gen_primary(sg, 1);
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
fprintf(stderr, "Writing unitig GFA to disk... \n");
fprintf(stderr, "Writing alternate contig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
sprintf(gfa_name, "%s.alter.ctg.gfa", output_file_name);
sprintf(gfa_name, "%s.a_ctg.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
// sprintf(gfa_name, "%s.simple.alter.ctg.gfa", output_file_name);
// output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
// fclose(output_file);
sprintf(gfa_name, "%s.a_ctg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);