X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcf.c;h=080b6fefcfc6ba8af057bd0a9792f620ac061f7a;hb=27eec65490fb3461f0af054868d9a0949e1843ed;hp=c3313881ef90fc2930c72d218c090b35e5cf9466;hpb=d77625704ad9a593a8ec60f7243d0cc1eebc855e;p=samtools.git

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index c331388..080b6fe 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 +13,9 @@ bcf_t *bcf_open(const char *fn, const char *mode)
 	} else {
 		b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
 	}
+#ifndef BCF_LITE
 	b->fp->owned_file = 1;
+#endif
 	return b;
 }
 
@@ -100,21 +96,27 @@ 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;
+	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;
@@ -136,8 +138,10 @@ int bcf_sync(int n_smpl, bcf1_t *b)
 			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 +150,12 @@ 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 +168,12 @@ 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 +181,7 @@ 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 +194,7 @@ 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);
@@ -215,7 +218,7 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_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);
+	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]) {
@@ -239,12 +242,26 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
 				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];
-				kputc('0' + (y>>3&7), s);
-				kputc("/|"[y>>6&1], s);
-				kputc('0' + (y&7), s);
-			}
+				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);
+					ksprintf(s, "%.2f", d[k]);
+				}
+			} else kputc('.', s); // custom fields
 		}
 	}
 }
@@ -256,3 +273,50 @@ char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
 	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 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;
+}