X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcf.c;h=87ff6c7435abc65758017bf3f6307df803e0606c;hb=74e6aebb5c07d14cdccc5f8abb40fd4a00b2be86;hp=f6c26f2db2e248c05ffefe34642a5a68b33ae95b;hpb=94027d8bf194b5e62b98d8a2b240a3ab1c439b46;p=samtools.git

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index f6c26f2..87ff6c7 100644
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -4,12 +4,6 @@
 #include "kstring.h"
 #include "bcf.h"
 
-void bcf_hdr_clear(bcf_hdr_t *b)
-{
-	free(b->name); free(b->sname); free(b->txt); free(b->ns); free(b->sns);
-	memset(b, 0, sizeof(bcf_hdr_t));
-}
-
 bcf_t *bcf_open(const char *fn, const char *mode)
 {
 	bcf_t *b;
@@ -19,7 +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;
 }
 
@@ -100,21 +93,33 @@ int bcf_hdr_sync(bcf_hdr_t *b)
 	return 0;
 }
 
-int bcf_sync(int n_smpl, bcf1_t *b)
+int bcf_sync(bcf1_t *b)
 {
 	char *p, *tmp[5];
-	int i, n;
+	int i, n, n_smpl = b->n_smpl;
 	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;
-	if (n != 5) return -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) 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];
 	// set n_alleles
-	for (p = b->alt, n = 1; *p; ++p)
-		if (*p == ',') ++n;
-	b->n_alleles = n + 1;
+	if (*b->alt == 0) b->n_alleles = 1;
+	else {
+		for (p = b->alt, n = 1; *p; ++p)
+			if (*p == ',') ++n;
+		b->n_alleles = n + 1;
+	}
 	// set n_gi and gi[i].fmt
 	for (p = b->fmt, n = 1; *p; ++p)
 		if (*p == ':') ++n;
@@ -132,12 +137,14 @@ int bcf_sync(int n_smpl, 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].len = 1;
-		} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+		} 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;
 		}
 		b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
 	}
@@ -146,13 +153,12 @@ int bcf_sync(int n_smpl, bcf1_t *b)
 
 int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
 {
-	uint32_t x;
 	int i, l = 0;
 	if (b == 0) return -1;
 	bgzf_write(bp->fp, &b->tid, 4);
 	bgzf_write(bp->fp, &b->pos, 4);
-	x = b->qual<<24 | b->l_str;
-	bgzf_write(bp->fp, &x, 4);
+	bgzf_write(bp->fp, &b->qual, 4);
+	bgzf_write(bp->fp, &b->l_str, 4);
 	bgzf_write(bp->fp, b->str, b->l_str);
 	l = 12 + b->l_str;
 	for (i = 0; i < b->n_gi; ++i) {
@@ -165,12 +171,12 @@ int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
 int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
 {
 	int i, l = 0;
-	uint32_t x;
 	if (b == 0) return -1;
 	if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
+	b->n_smpl = h->n_smpl;
 	bgzf_read(bp->fp, &b->pos, 4);
-	bgzf_read(bp->fp, &x, 4);
-	b->qual = x >> 24; b->l_str = x << 8 >> 8;
+	bgzf_read(bp->fp, &b->qual, 4);
+	bgzf_read(bp->fp, &b->l_str, 4);
 	if (b->l_str > b->m_str) {
 		b->m_str = b->l_str;
 		kroundup32(b->m_str);
@@ -178,7 +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(h->n_smpl, 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;
@@ -191,7 +197,7 @@ int bcf_destroy(bcf1_t *b)
 	int i;
 	if (b == 0) return -1;
 	free(b->str);
-	for (i = 0; i < b->n_gi; ++i)
+	for (i = 0; i < b->m_gi; ++i)
 		free(b->gi[i].data);
 	free(b->gi);
 	free(b);
@@ -204,41 +210,168 @@ static inline void fmt_str(const char *p, kstring_t *s)
 	else kputs(p, s);
 }
 
-char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
+void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
 {
-	kstring_t s;
 	int i, j, x;
-	memset(&s, 0, sizeof(kstring_t));
-	kputs(h->ns[b->tid], &s); kputc('\t', &s);
-	kputw(b->pos + 1, &s); kputc('\t', &s);
-	fmt_str(b->str, &s); kputc('\t', &s);
-	fmt_str(b->ref, &s); kputc('\t', &s);
-	fmt_str(b->alt, &s); kputc('\t', &s);
-	kputw(b->qual, &s); kputc('\t', &s);
-	fmt_str(b->flt, &s); kputc('\t', &s);
-	fmt_str(b->info, &s);
+	s->l = 0;
+	if (h->n_ref) kputs(h->ns[b->tid], s);
+	else kputw(b->tid, s);
+	kputc('\t', s);
+	kputw(b->pos + 1, s); kputc('\t', s);
+	fmt_str(b->str, s); kputc('\t', s);
+	fmt_str(b->ref, s); kputc('\t', s);
+	fmt_str(b->alt, s); kputc('\t', s);
+	ksprintf(s, "%.3g", b->qual); kputc('\t', s);
+	fmt_str(b->flt, s); kputc('\t', s);
+	fmt_str(b->info, s);
 	if (b->fmt[0]) {
-		kputc('\t', &s);
-		fmt_str(b->fmt, &s);
+		kputc('\t', s);
+		fmt_str(b->fmt, 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) {
-		kputc('\t', &s);
+        int ploidy = b->ploidy ? b->ploidy[j] : 2;
+		kputc('\t', s);
 		for (i = 0; i < b->n_gi; ++i) {
-			if (i) kputc(':', &s);
+			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;
+                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)) {
+				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 ( 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;
+				//printf("- %lx\n", d);
 				for (k = 0; k < x; ++k) {
-					if (k > 0) kputc(',', &s);
-					kputw(d[k], &s);
+					if (k > 0) kputc(',', s);
+					ksprintf(s, "%.2f", d[k]);
 				}
-			} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
-				kputw(((uint16_t*)b->gi[i].data)[j], &s);
-			} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
-				kputw(((uint8_t*)b->gi[i].data)[j], &s);
-			}
+			} else kputc('.', s); // custom fields
 		}
 	}
+}
+
+char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
+{
+	kstring_t s;
+	s.l = s.m = 0; s.s = 0;
+	bcf_fmt_core(h, b, &s);
 	return s.s;
 }
+
+int bcf_append_info(bcf1_t *b, const char *info, int l)
+{
+	int shift = b->fmt - b->str;
+	int l_fmt = b->l_str - shift;
+	char *ori = b->str;
+	if (b->l_str + l > b->m_str) { // enlarge if necessary
+		b->m_str = b->l_str + l;
+		kroundup32(b->m_str);
+		b->str = realloc(b->str, b->m_str);
+	}
+	memmove(b->str + shift + l, b->str + shift, l_fmt); // move the FORMAT field
+	memcpy(b->str + shift - 1, info, l); // append to the INFO field
+	b->str[shift + l - 1] = '\0';
+	b->fmt = b->str + shift + l;
+	b->l_str += l;
+	if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
+	return 0;
+}
+
+int remove_tag(char *str, 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++;
+        len_diff += q-p;
+        if ( ! *q ) { *p = 0; break; }
+        else
+            memmove(p,q,ori_len-(int)(q-p)+1);
+    }
+    if ( len_diff==ori_len )
+        str[0]='.', str[1]=0, len_diff--;
+
+    return len_diff;
+}
+
+int bcf_cpy(bcf1_t *r, const bcf1_t *b)
+{
+	char *t1 = r->str;
+	bcf_ginfo_t *t2 = r->gi;
+	int i, t3 = r->m_str, t4 = r->m_gi;
+	*r = *b;
+	r->str = t1; r->gi = t2; r->m_str = t3; r->m_gi = t4;
+	if (r->m_str < b->m_str) {
+		r->m_str = b->m_str;
+		r->str = realloc(r->str, r->m_str);
+	}
+	memcpy(r->str, b->str, r->m_str);
+	bcf_sync(r); // calling bcf_sync() is simple but inefficient
+	for (i = 0; i < r->n_gi; ++i)
+		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;
+}