X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcfutils.c;h=7638085d4ffacce35f26b401ff1a90f48a975454;hb=7c3295ba455fdc9269156dd1246c92ea5df3efd4;hp=91cc2c23ccb33c66c944fe013df1e92a84867858;hpb=d382711a770f67a72b9af3bfd98a88fbced34f64;p=samtools.git

diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index 91cc2c2..7638085 100644
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -1,10 +1,17 @@
 #include <string.h>
 #include <math.h>
+#include <assert.h>
 #include "bcf.h"
 #include "kstring.h"
 #include "khash.h"
 KHASH_MAP_INIT_STR(str2id, int)
 
+#ifdef _WIN32
+#define srand48(x) srand(x)
+#define drand48() ((double)rand() / RAND_MAX)
+#endif
+
+// FIXME: valgrind report a memory leak in this function. Probably it does not get deallocated...
 void *bcf_build_refhash(bcf_hdr_t *h)
 {
 	khash_t(str2id) *hash;
@@ -60,6 +67,112 @@ int bcf_str2id_add(void *_hash, const char *str)
 	return kh_val(hash, k);
 }
 
+void bcf_fit_alt(bcf1_t *b, int mask)
+{
+    mask |= 1; // REF must be always present
+
+    int i,j,nals=0;
+    for (i=0; i<sizeof(int); i++)
+        if ( mask&1<<i) nals++;
+    if ( b->n_alleles <= nals ) return;
+
+    // update ALT, in principle any of the alleles can be removed
+    char *p;
+    if ( nals>1 ) 
+    {
+        char *dst, *src;
+        int n=0, nalts=nals-1;
+        for (src=dst=p=b->alt, i=1; *p; p++)
+        {
+            if ( *p!=',' ) continue;
+
+            if ( mask&1<<i )
+            {
+                n++;
+                if ( src!=dst )
+                {
+                    memmove(dst,src,p-src);
+                    dst += p-src;
+                }
+                else dst = p;
+                if ( n<nalts ) { *dst=','; dst++; }
+            }
+            i++;
+
+            if ( n>=nalts ) { *dst=0; break; }
+            src = p+1;
+        }
+        if ( n<nalts )
+        {
+            memmove(dst,src,p-src);
+            dst += p-src;
+            *dst = 0;
+        }
+        p = dst;
+    }
+    else p = b->alt, *p = '\0';
+    p++;
+    memmove(p, b->flt, b->str + b->l_str - b->flt);
+    b->l_str -= b->flt - p;
+
+    // update PL and GT
+    int ipl=-1, igt=-1;
+    for (i = 0; i < b->n_gi; ++i) 
+    {
+        bcf_ginfo_t *g = b->gi + i;
+        if (g->fmt == bcf_str2int("PL", 2)) ipl = i;
+        if (g->fmt == bcf_str2int("GT", 2)) igt = i;
+    }
+
+    // .. create mapping between old and new indexes
+    int npl = nals * (nals+1) / 2;
+    int *map = malloc(sizeof(int)*(npl>b->n_alleles ? npl : b->n_alleles));
+    int kori=0,knew=0;
+    for (i=0; i<b->n_alleles; i++)
+    {
+        for (j=0; j<=i; j++)
+        {
+            int skip=0;
+            if ( i && !(mask&1<<i) ) skip=1;
+            if ( j && !(mask&1<<j) ) skip=1;
+            if ( !skip ) { map[knew++] = kori; }
+            kori++;
+        }
+    }
+    // .. apply to all samples
+    int n_smpl = b->n_smpl;
+    for (i = 0; i < b->n_gi; ++i) 
+    {
+        bcf_ginfo_t *g = b->gi + i;
+        if (g->fmt == bcf_str2int("PL", 2)) 
+        {
+            g->len = npl;
+            uint8_t *d = (uint8_t*)g->data;
+            int ismpl, npl_ori = b->n_alleles * (b->n_alleles + 1) / 2;
+            for (knew=ismpl=0; ismpl<n_smpl; ismpl++)
+            {
+                uint8_t *dl = d + ismpl * npl_ori;
+                for (j=0; j<npl; j++) d[knew++] = dl[map[j]];
+            }
+        } // FIXME: to add GL
+    }
+    // update GTs
+    map[0] = 0;
+    for (i=1, knew=0; i<b->n_alleles; i++)
+        map[i] = mask&1<<i ? ++knew : -1;
+    for (i=0; i<n_smpl; i++)
+    {
+        uint8_t gt = ((uint8_t*)b->gi[igt].data)[i];
+        int a1 = (gt>>3)&7;
+        int a2 = gt&7;
+        assert( map[a1]>=0 && map[a2]>=0 );
+        ((uint8_t*)b->gi[igt].data)[i] = ((1<<7|1<<6)&gt) | map[a1]<<3 | map[a2];
+    }
+    free(map);
+    b->n_alleles = nals;
+    bcf_sync(b);
+}
+
 int bcf_shrink_alt(bcf1_t *b, int n)
 {
 	char *p;
@@ -127,7 +240,7 @@ int bcf_fix_gt(bcf1_t *b)
 	bcf_ginfo_t gt;
 	// check the presence of the GT FMT
 	if ((s = strstr(b->fmt, ":GT")) == 0) return 0; // no GT or GT is already the first
-	if (s[3] != '\0' && s[3] != ':') return 0; // :GTX in fact
+	assert(s[3] == '\0' || s[3] == ':'); // :GTX in fact
 	tmp = bcf_str2int("GT", 2);
 	for (i = 0; i < b->n_gi; ++i)
 		if (b->gi[i].fmt == tmp) break;
@@ -136,7 +249,10 @@ int bcf_fix_gt(bcf1_t *b)
 	// move GT to the first
 	for (; i > 0; --i) b->gi[i] = b->gi[i-1];
 	b->gi[0] = gt;
-	memmove(b->fmt + 3, b->fmt, s + 1 - b->fmt);
+    if ( s[3]==0 )
+        memmove(b->fmt + 3, b->fmt, s - b->fmt);        // :GT
+    else
+        memmove(b->fmt + 3, b->fmt, s - b->fmt + 1);    // :GT:
 	b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
 	return 0;
 }
@@ -168,6 +284,27 @@ int bcf_fix_pl(bcf1_t *b)
 	return 0;
 }
 
+int bcf_smpl_covered(const bcf1_t *b)
+{
+	int i, j, n = 0;
+	uint32_t tmp;
+	bcf_ginfo_t *gi;
+	// pinpoint PL
+	tmp = bcf_str2int("PL", 2);
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == tmp) break;
+	if (i == b->n_gi) return 0;
+	// count how many samples having PL!=[0..0]
+	gi = b->gi + i;
+	for (i = 0; i < b->n_smpl; ++i) {
+		uint8_t *PLi = ((uint8_t*)gi->data) + i * gi->len;
+		for (j = 0; j < gi->len; ++j)
+			if (PLi[j]) break;
+		if (j < gi->len) ++n;
+	}
+	return n;
+}
+
 static void *locate_field(const bcf1_t *b, const char *fmt, int l)
 {
 	int i;
@@ -260,7 +397,11 @@ bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int
 			kputs(samples[i], &s); kputc('\0', &s);
 		}
 	}
-	if (j < n) fprintf(stderr, "<%s> %d samples in the list but not in BCF.", __func__, n - j);
+	if (j < n) 
+    {
+        fprintf(stderr, "<%s> %d samples in the list but not in BCF.", __func__, n - j);
+        exit(1);
+    }
 	kh_destroy(str2id, hash);
 	h = calloc(1, sizeof(bcf_hdr_t));
 	*h = *h0;
@@ -287,3 +428,77 @@ int bcf_subsam(int n_smpl, int *list, bcf1_t *b)
 	b->n_smpl = n_smpl;
 	return 0;
 }
+
+static int8_t nt4_table[128] = {
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4 /*'-'*/, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  3, 4, 4, 4, -1, 4, 4, 4,  4, 4, 4, 4, 
+	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  3, 4, 4, 4, -1, 4, 4, 4,  4, 4, 4, 4
+};
+
+int bcf_gl10(const bcf1_t *b, uint8_t *gl)
+{
+	int a[4], k, l, map[4], k1, j, i;
+	const bcf_ginfo_t *PL;
+	char *s;
+	if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base or >4 alleles
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+	if (i == b->n_gi) return -1; // no PL
+	PL = b->gi + i;
+	a[0] = nt4_table[(int)b->ref[0]];
+	if (a[0] > 3 || a[0] < 0) return -1; // ref is not A/C/G/T
+	a[1] = a[2] = a[3] = -2; // -1 has a special meaning
+	if (b->alt[0] == 0) return -1; // no alternate allele
+	map[0] = map[1] = map[2] = map[3] = -2;
+	map[a[0]] = 0;
+	for (k = 0, s = b->alt, k1 = -1; k < 3 && *s; ++k, s += 2) {
+		if (s[1] != ',' && s[1] != 0) return -1; // ALT is not single base
+		a[k+1] = nt4_table[(int)*s];
+		if (a[k+1] >= 0) map[a[k+1]] = k+1;
+		else k1 = k + 1;
+		if (s[1] == 0) break; // the end of the ALT string
+	}
+	for (k = 0; k < 4; ++k)
+		if (map[k] < 0) map[k] = k1;
+	for (i = 0; i < b->n_smpl; ++i) {
+		const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
+		uint8_t *g = gl + 10 * i;
+		for (k = j = 0; k < 4; ++k) {
+			for (l = k; l < 4; ++l) {
+				int t, x = map[k], y = map[l];
+				if (x > y) t = x, x = y, y = t; // make sure x is the smaller
+				g[j++] = p[y * (y+1) / 2 + x];
+			}
+		}
+	}
+	return 0;
+}
+
+int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl)
+{
+	int k, l, j, i;
+	const bcf_ginfo_t *PL;
+	if (b->alt[0] == 0) return -1; // no alternate allele
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+	if (i == b->n_gi) return -1; // no PL
+	PL = b->gi + i;
+	for (i = 0; i < b->n_smpl; ++i) {
+		const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
+		uint8_t *g = gl + 10 * i;
+		for (k = j = 0; k < 4; ++k) {
+			for (l = k; l < 4; ++l) {
+				int t, x = k, y = l;
+				if (x > y) t = x, x = y, y = t; // make sure x is the smaller
+				x = y * (y+1) / 2 + x;
+				g[j++] = x < PL->len? p[x] : 255;
+			}
+		}
+	}
+	return 0;
+}