X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=sam%2Fbcftools%2Fbcfutils.c;h=7638085d4ffacce35f26b401ff1a90f48a975454;hp=4d6835da8206ea96542ce66e14124b4a388e70db;hb=dbcf1cfb8ad1086c21d64e249f012809403e7ddc;hpb=2e4fdfb2673d928779b04bc5ebe8fcb304a45eaa

diff --git a/sam/bcftools/bcfutils.c b/sam/bcftools/bcfutils.c
index 4d6835d..7638085 100644
--- a/sam/bcftools/bcfutils.c
+++ b/sam/bcftools/bcfutils.c
@@ -1,8 +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;
@@ -27,6 +36,16 @@ void bcf_str2id_destroy(void *_hash)
 	if (hash) kh_destroy(str2id, hash); // Note that strings are not freed.
 }
 
+void bcf_str2id_thorough_destroy(void *_hash)
+{
+	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+	khint_t k;
+	if (hash == 0) return;
+	for (k = 0; k < kh_end(hash); ++k)
+		if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
+	kh_destroy(str2id, hash);
+}
+
 int bcf_str2id(void *_hash, const char *str)
 {
 	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
@@ -48,11 +67,118 @@ 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;
-	int i, j, k, *z, n_smpl = b->n_smpl;
+	int i, j, k, n_smpl = b->n_smpl;
 	if (b->n_alleles <= n) return -1;
+	// update ALT
 	if (n > 1) {
 		for (p = b->alt, k = 1; *p; ++p)
 			if (*p == ',' && ++k == n) break;
@@ -61,10 +187,7 @@ int bcf_shrink_alt(bcf1_t *b, int n)
 	++p;
 	memmove(p, b->flt, b->str + b->l_str - b->flt);
 	b->l_str -= b->flt - p;
-	z = alloca(sizeof(int) / 2 * n * (n+1));
-	for (i = k = 0; i < n; ++i)
-		for (j = 0; j < n - i; ++j)
-			z[k++] = i * b->n_alleles + j;
+	// update PL
 	for (i = 0; i < b->n_gi; ++i) {
 		bcf_ginfo_t *g = b->gi + i;
 		if (g->fmt == bcf_str2int("PL", 2)) {
@@ -73,7 +196,7 @@ int bcf_shrink_alt(bcf1_t *b, int n)
 			g->len = n * (n + 1) / 2;
 			for (l = k = 0; l < n_smpl; ++l) {
 				uint8_t *dl = d + l * x;
-				for (j = 0; j < g->len; ++j) d[k++] = dl[z[j]];
+				for (j = 0; j < g->len; ++j) d[k++] = dl[j];
 			}
 		} // FIXME: to add GL
 	}
@@ -107,3 +230,275 @@ int bcf_gl2pl(bcf1_t *b)
 	}
 	return 0;
 }
+/* FIXME: this function will fail given AB:GTX:GT. BCFtools never
+ * produces such FMT, but others may do. */
+int bcf_fix_gt(bcf1_t *b)
+{
+	char *s;
+	int i;
+	uint32_t tmp;
+	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
+	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;
+	if (i == b->n_gi) return 0; // no GT in b->gi; probably a bug...
+	gt = b->gi[i];
+	// move GT to the first
+	for (; i > 0; --i) b->gi[i] = b->gi[i-1];
+	b->gi[0] = gt;
+    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;
+}
+
+int bcf_fix_pl(bcf1_t *b)
+{
+	int i;
+	uint32_t tmp;
+	uint8_t *PL, *swap;
+	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;
+	// prepare
+	gi = b->gi + i;
+	PL = (uint8_t*)gi->data;
+	swap = alloca(gi->len);
+	// loop through individuals
+	for (i = 0; i < b->n_smpl; ++i) {
+		int k, l, x;
+		uint8_t *PLi = PL + i * gi->len;
+		memcpy(swap, PLi, gi->len);
+		for (k = x = 0; k < b->n_alleles; ++k)
+			for (l = k; l < b->n_alleles; ++l)
+				PLi[l*(l+1)/2 + k] = swap[x++];
+	}
+	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;
+	uint32_t tmp;
+	tmp = bcf_str2int(fmt, l);
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == tmp) break;
+	return i == b->n_gi? 0 : b->gi[i].data;
+}
+
+int bcf_anno_max(bcf1_t *b)
+{
+	int k, max_gq, max_sp, n_het;
+	kstring_t str;
+	uint8_t *gt, *gq;
+	int32_t *sp;
+	max_gq = max_sp = n_het = 0;
+	gt = locate_field(b, "GT", 2);
+	if (gt == 0) return -1;
+	gq = locate_field(b, "GQ", 2);
+	sp = locate_field(b, "SP", 2);
+	if (sp)
+		for (k = 0; k < b->n_smpl; ++k)
+			if (gt[k]&0x3f)
+				max_sp = max_sp > (int)sp[k]? max_sp : sp[k];
+	if (gq)
+		for (k = 0; k < b->n_smpl; ++k)
+			if (gt[k]&0x3f)
+				max_gq = max_gq > (int)gq[k]? max_gq : gq[k];
+	for (k = 0; k < b->n_smpl; ++k) {
+		int a1, a2;
+		a1 = gt[k]&7; a2 = gt[k]>>3&7;
+		if ((!a1 && a2) || (!a2 && a1)) { // a het
+			if (gq == 0) ++n_het;
+			else if (gq[k] >= 20) ++n_het;
+		}
+	}
+	if (n_het) max_sp -= (int)(4.343 * log(n_het) + .499);
+	if (max_sp < 0) max_sp = 0;
+	memset(&str, 0, sizeof(kstring_t));
+	if (*b->info) kputc(';', &str);
+	ksprintf(&str, "MXSP=%d;MXGQ=%d", max_sp, max_gq);
+	bcf_append_info(b, str.s, str.l);
+	free(str.s);
+	return 0;
+}
+
+// FIXME: only data are shuffled; the header is NOT
+int bcf_shuffle(bcf1_t *b, int seed)
+{
+	int i, j, *a;
+	if (seed > 0) srand48(seed);
+	a = malloc(b->n_smpl * sizeof(int));
+	for (i = 0; i < b->n_smpl; ++i) a[i] = i;
+	for (i = b->n_smpl; i > 1; --i) {
+		int tmp;
+		j = (int)(drand48() * i);
+		tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;
+	}
+	for (j = 0; j < b->n_gi; ++j) {
+		bcf_ginfo_t *gi = b->gi + j;
+		uint8_t *swap, *data = (uint8_t*)gi->data;
+		swap = malloc(gi->len * b->n_smpl);
+		for (i = 0; i < b->n_smpl; ++i)
+			memcpy(swap + gi->len * a[i], data + gi->len * i, gi->len);
+		free(gi->data);
+		gi->data = swap;
+	}
+	free(a);
+	return 0;
+}
+
+bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list)
+{
+	int i, ret, j;
+	khint_t k;
+	bcf_hdr_t *h;
+	khash_t(str2id) *hash;
+	kstring_t s;
+	s.l = s.m = 0; s.s = 0;
+	hash = kh_init(str2id);
+	for (i = 0; i < h0->n_smpl; ++i) {
+		k = kh_put(str2id, hash, h0->sns[i], &ret);
+		kh_val(hash, k) = i;
+	}
+	for (i = j = 0; i < n; ++i) {
+		k = kh_get(str2id, hash, samples[i]);
+		if (k != kh_end(hash)) {
+			list[j++] = kh_val(hash, k);
+			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);
+        exit(1);
+    }
+	kh_destroy(str2id, hash);
+	h = calloc(1, sizeof(bcf_hdr_t));
+	*h = *h0;
+	h->ns = 0; h->sns = 0;
+	h->name = malloc(h->l_nm); memcpy(h->name, h0->name, h->l_nm);
+	h->txt = calloc(1, h->l_txt + 1); memcpy(h->txt, h0->txt, h->l_txt);
+	h->l_smpl = s.l; h->sname = s.s;
+	bcf_hdr_sync(h);
+	return h;
+}
+
+int bcf_subsam(int n_smpl, int *list, bcf1_t *b)
+{
+	int i, j;
+	for (j = 0; j < b->n_gi; ++j) {
+		bcf_ginfo_t *gi = b->gi + j;
+		uint8_t *swap;
+		swap = malloc(gi->len * b->n_smpl);
+		for (i = 0; i < n_smpl; ++i)
+			memcpy(swap + i * gi->len, (uint8_t*)gi->data + list[i] * gi->len, gi->len);
+		free(gi->data);
+		gi->data = swap;
+	}
+	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;
+}