X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcf.c;h=3393aad1edef67c24c548dbc290b15ac02c14caf;hb=221f82f662dd770a17d1bd2181de46b8c3b3fdfd;hp=f6c26f2db2e248c05ffefe34642a5a68b33ae95b;hpb=94027d8bf194b5e62b98d8a2b240a3ab1c439b46;p=samtools.git

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index f6c26f2..3393aad 100644
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -109,12 +109,18 @@ int bcf_sync(int n_smpl, bcf1_t *b)
 	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, "[bcf_sync] incorrect number of fields (%d != 5)\n", n);
+		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;
@@ -137,7 +143,7 @@ int bcf_sync(int n_smpl, bcf1_t *b)
 		} 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)) {
-			b->gi[i].len = 4;
+			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 +152,12 @@ 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 +170,11 @@ 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;
 	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);
@@ -204,41 +208,67 @@ 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); /*kputw(b->qual, s);*/ 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;
 	for (j = 0; j < h->n_smpl; ++j) {
-		kputc('\t', &s);
+		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;
 				for (k = 0; k < x; ++k) {
-					if (k > 0) kputc(',', &s);
-					kputw(d[k], &s);
+					if (k > 0) kputc(',', s);
+					kputw(d[k], s);
 				}
 			} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
-				kputw(((uint16_t*)b->gi[i].data)[j], &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);
+				kputw(((uint8_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);
+				}
+			} 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]);
+				}
 			}
 		}
 	}
+}
+
+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;
 }