VCF annotations with and without -m and more robust rm_info

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 035eddc70386bd011f710970026e50358a502be4..6695c74226059ea55033792dabab3faba4dbda05 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -13,7 +13,6 @@ bcf_t *bcf_open(const char *fn, const char *mode)
        } else {
                b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
        }
-       b->fp->owned_file = 1;
        return b;
 }
 
@@ -101,10 +100,16 @@ int bcf_sync(bcf1_t *b)
        ks_tokaux_t aux;
        // set ref, alt, flt, info, fmt
        b->ref = b->alt = b->flt = b->info = b->fmt = 0;
-       for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
-               if (*p == 0 && p+1 != b->str + b->l_str) tmp[n++] = p + 1;
+       for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
+               if (*p == 0 && p+1 != b->str + b->l_str) {
+                       if (n == 5) {
+                               ++n;
+                               break;
+                       } else tmp[n++] = p + 1;
+               }
+       }
        if (n != 5) {
-               fprintf(stderr, "[%s] incorrect number of fields (%d != 5). Corrupted file?\n", __func__, n);
+               fprintf(stderr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
                return -1;
        }
        b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
@@ -132,12 +137,12 @@ int bcf_sync(bcf1_t *b)
        for (i = 0; i < b->n_gi; ++i) {
                if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
                        b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
-               } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
+               } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
                        b->gi[i].len = 2;
-               } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)
-                                  || b->gi[i].fmt == bcf_str2int("ST", 2))
-               {
+               } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
                        b->gi[i].len = 1;
+               } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+                       b->gi[i].len = 4;
                } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
                        b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
                }
@@ -179,7 +184,7 @@ int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
        }
        bgzf_read(bp->fp, b->str, b->l_str);
        l = 12 + b->l_str;
-       bcf_sync(b);
+       if (bcf_sync(b) < 0) return -2;
        for (i = 0; i < b->n_gi; ++i) {
                bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
                l += b->gi[i].len * h->n_smpl;
@@ -225,30 +230,59 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
        }
        x = b->n_alleles * (b->n_alleles + 1) / 2;
        if (b->n_gi == 0) return;
+    int iPL = -1;
+    if ( b->n_alleles > 2 ) {
+        for (i=0; i<b->n_gi; i++) {
+            if ( b->gi[i].fmt == bcf_str2int("PL", 2) ) {
+                iPL = i;
+                break;
+            }
+        }
+    }
        for (j = 0; j < h->n_smpl; ++j) {
+        int ploidy = b->ploidy ? b->ploidy[j] : 2;
                kputc('\t', s);
                for (i = 0; i < b->n_gi; ++i) {
                        if (i) kputc(':', s);
                        if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
                                uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
                                int k;
-                               for (k = 0; k < x; ++k) {
-                                       if (k > 0) kputc(',', s);
-                                       kputw(d[k], s);
-                               }
-                       } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+                if ( ploidy==1 )
+                    for (k=0; k<b->n_alleles; k++)
+                    {
+                        if (k>0) kputc(',', s);
+                        kputw(d[(k+1)*(k+2)/2-1], s);
+                    }
+                else
+                    for (k = 0; k < x; ++k) {
+                        if (k > 0) kputc(',', s);
+                        kputw(d[k], s);
+                    }
+                       } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
                                kputw(((uint16_t*)b->gi[i].data)[j], s);
-                       } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("ST", 2)) {
+                       } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
                                kputw(((uint8_t*)b->gi[i].data)[j], s);
+                       } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+                               kputw(((int32_t*)b->gi[i].data)[j], s);
                        } else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
-                               int y = ((uint8_t*)b->gi[i].data)[j];
-                               if (y>>7&1) {
-                                       kputsn("./.", 3, s);
-                               } else {
-                                       kputc('0' + (y>>3&7), s);
-                                       kputc("/|"[y>>6&1], s);
-                                       kputc('0' + (y&7), s);
-                               }
+                int y = ((uint8_t*)b->gi[i].data)[j];
+                if ( ploidy==1 )
+                {
+                    if ( y>>7&1 )
+                        kputsn(".", 3, s);
+                    else 
+                        kputc('0' + (y>>3&7), s);
+                }
+                else
+                {
+                    if ( y>>7&1 )
+                        kputsn("./.", 3, s);
+                    else { 
+                        kputc('0' + (y>>3&7), s);
+                        kputc("/|"[y>>6&1], s);
+                        kputc('0' + (y&7), s);
+                    }
+                }
                        } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
                                float *d = (float*)b->gi[i].data + j * x;
                                int k;
@@ -257,7 +291,7 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
                                        if (k > 0) kputc(',', s);
                                        ksprintf(s, "%.2f", d[k]);
                                }
-                       }
+                       } else kputc('.', s); // custom fields
                }
        }
 }
@@ -289,6 +323,50 @@ int bcf_append_info(bcf1_t *b, const char *info, int l)
        return 0;
 }
 
+int remove_tag(char *str, const char *tag, char delim)
+{
+    char *tmp = str, *p;
+    int len_diff = 0, ori_len = strlen(str);
+    while ( *tmp && (p = strstr(tmp,tag)) )
+    {
+        if ( p>str )
+        {
+            if ( *(p-1)!=delim ) { tmp=p+1; continue; } // shared substring
+            p--;
+        }
+        char *q=p+1;
+        while ( *q && *q!=delim ) q++;
+        if ( p==str && *q ) q++;        // the tag is first, don't move the delim char
+        len_diff += q-p;
+        if ( ! *q ) { *p = 0; break; }  // the tag was last, no delim follows
+        else
+            memmove(p,q,ori_len-(int)(p-str)-(int)(q-p)-1);  // *q==delim
+    }
+    if ( len_diff==ori_len )
+        str[0]='.', str[1]=0, len_diff--;
+
+    return len_diff;
+}
+
+
+void rm_info(kstring_t *s, const char *key)
+{
+    char *p = s->s; 
+    int n = 0;
+    while ( n<4 )
+    {
+        if ( !*p ) n++;
+        p++;
+    }
+    char *q = p+1; 
+    while ( *q && q-s->s<s->l ) q++;
+
+    int nrm = remove_tag(p, key, ';');
+    if ( nrm )
+        memmove(q-nrm, q, s->s+s->l-q+1);
+    s->l -= nrm;
+}
+
 int bcf_cpy(bcf1_t *r, const bcf1_t *b)
 {
        char *t1 = r->str;
@@ -306,3 +384,13 @@ int bcf_cpy(bcf1_t *r, const bcf1_t *b)
                memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
        return 0;
 }
+
+int bcf_is_indel(const bcf1_t *b)
+{
+       char *p;
+       if (strlen(b->ref) > 1) return 1;
+       for (p = b->alt; *p; ++p)
+               if (*p != ',' && p[1] != ',' && p[1] != '\0')
+                       return 1;
+       return 0;
+}