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integration/print het sites

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chhylp123
2022-01-17 18:29:48 -05:00
parent 7af0d85258
commit 0ce5a7ba5b
18 changed files with 2884 additions and 385 deletions
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Overlaps.cpp
+6 -8
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@@ -9757,19 +9757,17 @@ uint64_t *n_utg)
void ma_ug_print2(const ma_ug_t *ug, All_reads *RNF, asg_t* read_g, const ma_sub_t *coverage_cut,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int print_seq, const char* prefix, FILE *fp)
{
uint8_t* primary_flag = (uint8_t*)calloc(read_g->n_seq, sizeof(uint8_t));
uint32_t i, j, l;
uint8_t* primary_flag = read_g?(uint8_t*)calloc(read_g->n_seq, sizeof(uint8_t)):NULL;
uint32_t i, j, l, pc = read_g && coverage_cut && sources && ruIndex?1:0;
char name[32];
for (i = 0; i < ug->u.n; ++i) { // the Segment lines in GFA
ma_utg_t *p = &ug->u.a[i];
if(p->m == 0) continue;
sprintf(name, "%s%.6d%c", prefix, i + 1, "lc"[p->circ]);
if (print_seq) fprintf(fp, "S\t%s\t%s\tLN:i:%d\trd:i:%u\n", name, p->s? p->s : "*", p->len,
get_ug_coverage(p, read_g, coverage_cut, sources, ruIndex, primary_flag));
pc?get_ug_coverage(p, read_g, coverage_cut, sources, ruIndex, primary_flag):0);
else fprintf(fp, "S\t%s\t*\tLN:i:%d\trd:i:%u\n", name, p->len,
get_ug_coverage(p, read_g, coverage_cut, sources, ruIndex, primary_flag));
// 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);
pc?get_ug_coverage(p, read_g, coverage_cut, sources, ruIndex, primary_flag):0);
for (j = l = 0; j < p->n; j++) {
if(p->a[j] != (uint64_t)-1)
@@ -9779,13 +9777,13 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int print_seq, const char* prefix, FIL
{
fprintf(fp, "A\t%s\t%d\t%c\t%.*s\t%d\t%d\tid:i:%d\tHG:A:%c\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,
coverage_cut?coverage_cut[x].s:0, coverage_cut?coverage_cut[x].e:(int)Get_READ_LENGTH((*RNF), x), x,
"apmaaa"[((RNF->trio_flag[x]!=FATHER && RNF->trio_flag[x]!=MOTHER)?AMBIGU:RNF->trio_flag[x])]);
}
else
{
fprintf(fp, "A\t%s\t%d\t%c\t%s\t%d\t%d\tid:i:%d\tHG:A:%c\n", name, l, "+-"[p->a[j]>>32&1],
"FAKE", coverage_cut[x].s, coverage_cut[x].e, x, '*');
"FAKE", coverage_cut?coverage_cut[x].s:0, coverage_cut?coverage_cut[x].e:(int)Get_READ_LENGTH((*RNF), x), x, '*');
}
}
else