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r309: improved SAM header output

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This commit is contained in:
Heng Li
2017-08-25 10:35:58 +08:00
parent 240f6caaff
commit 0fe1a224ab
9 changed files with 61 additions and 42 deletions
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format.c
+27 -19
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@@ -6,7 +6,7 @@
#include "kalloc.h"
#include "mmpriv.h"
static char *mm_rg_line, mm_rg_id[256];
static char mm_rg_id[256];
static inline void str_enlarge(kstring_t *s, int l)
{
@@ -58,15 +58,13 @@ static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
s->s[s->l] = 0;
}
static inline char *mm_escape(char *s)
static char *mm_escape(char *s)
{
char *p, *q;
for (p = q = s; *p; ++p) {
if (*p == '\\') {
++p;
if (*p == 't') *q++ = '\t';
else if (*p == 'n') *q++ = '\n';
else if (*p == 'r') *q++ = '\r';
else if (*p == '\\') *q++ = '\\';
} else *q++ = *p;
}
@@ -74,44 +72,56 @@ static inline char *mm_escape(char *s)
return s;
}
void mm_set_rg(const char *s)
static void sam_write_rg_line(kstring_t *str, const char *s)
{
char *p, *q, *r, *rg_line = 0;
memset(mm_rg_id, 0, 256);
if (mm_rg_line) {
free(mm_rg_line);
mm_rg_line = 0;
}
if (s == 0) return;
if (strstr(s, "@RG") != s) {
if (mm_verbose >= 1) fprintf(stderr, "[E::%s] the read group line is not started with @RG\n", __func__);
if (mm_verbose >= 1) fprintf(stderr, "[ERROR] the read group line is not started with @RG\n");
goto err_set_rg;
}
if (strstr(s, "\t") != NULL) {
if (mm_verbose >= 1) fprintf(stderr, "[E::%s] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\n", __func__);
if (mm_verbose >= 1) fprintf(stderr, "[ERROR] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\n");
goto err_set_rg;
}
rg_line = strdup(s);
mm_escape(rg_line);
if ((p = strstr(rg_line, "\tID:")) == 0) {
if (mm_verbose >= 1) fprintf(stderr, "[E::%s] no ID within the read group line\n", __func__);
if (mm_verbose >= 1) fprintf(stderr, "[ERROR] no ID within the read group line\n");
goto err_set_rg;
}
p += 4;
for (q = p; *q && *q != '\t' && *q != '\n'; ++q);
if (q - p + 1 > 256) {
if (mm_verbose >= 1) fprintf(stderr, "[E::%s] @RG:ID is longer than 255 characters\n", __func__);
if (mm_verbose >= 1) fprintf(stderr, "[ERROR] @RG:ID is longer than 255 characters\n");
goto err_set_rg;
}
for (q = p, r = mm_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
*r++ = *q;
mm_rg_line = rg_line;
return;
mm_sprintf_lite(str, "%s\n", rg_line);
err_set_rg:
free(rg_line);
}
void mm_write_sam_hdr_no_SQ(const char *rg, const char *ver, int argc, char *argv[])
{
kstring_t str = {0,0,0};
sam_write_rg_line(&str, rg);
mm_sprintf_lite(&str, "@PG\tID:minimap2\tPN:minimap2");
if (ver) mm_sprintf_lite(&str, "\tVN:%s", ver);
if (argc > 1) {
int i;
mm_sprintf_lite(&str, "\tCL:minimap2");
for (i = 1; i < argc; ++i)
mm_sprintf_lite(&str, " %s", argv[i]);
}
mm_sprintf_lite(&str, "\n");
fputs(str.s, stdout);
free(str.s);
}
static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
{
extern unsigned char seq_nt4_table[256];
@@ -214,12 +224,11 @@ static char comp_tab[] = {
'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127
};
void sam_write_sam_header(const mm_idx_t *idx)
void mm_write_sam_SQ(const mm_idx_t *idx)
{
uint32_t i;
for (i = 0; i < idx->n_seq; ++i)
printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
if (mm_rg_line) puts(mm_rg_line);
}
static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
@@ -274,8 +283,7 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
else mm_sprintf_lite(s, "*");
}
write_tags(s, r);
if (mm_rg_line && mm_rg_id[0])
mm_sprintf_lite(s, "\tRG:Z:%s", mm_rg_id);
if (mm_rg_id[0]) mm_sprintf_lite(s, "\tRG:Z:%s", mm_rg_id);
if (r->parent == r->id && r->p && n_regs > 1 && regs && r >= regs && r - regs < n_regs) { // supplementary aln may exist
int i, n_sa = 0; // n_sa: number of SA fields
for (i = 0; i < n_regs; ++i)