X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam%2Fbcftools%2Fbcf.c;fp=sam%2Fbcftools%2Fbcf.c;h=24728dbe1515e7cc1171a8cc08f842bafa167d5e;hb=dbcf1cfb8ad1086c21d64e249f012809403e7ddc;hp=84a8e767ec58adb397630f609a52670779f99c89;hpb=58d504aaf36ae486b1dba6d03e0e9f1c25855037;p=rsem.git

diff --git a/sam/bcftools/bcf.c b/sam/bcftools/bcf.c
index 84a8e76..24728db 100644
--- a/sam/bcftools/bcf.c
+++ b/sam/bcftools/bcf.c
@@ -13,9 +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);
 	}
-#ifndef BCF_LITE
-	b->fp->owned_file = 1;
-#endif
 	return b;
 }
 
@@ -140,7 +137,7 @@ int bcf_sync(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;
@@ -233,32 +230,59 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *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) {
+        int ploidy = b->ploidy ? b->ploidy[j] : 2;
 		kputc('\t', s);
 		for (i = 0; i < b->n_gi; ++i) {
 			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);
-				}
-			} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+                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 (y>>7&1) {
-					kputsn("./.", 3, s);
-				} else {
-					kputc('0' + (y>>3&7), s);
-					kputc("/|"[y>>6&1], s);
-					kputc('0' + (y&7), s);
-				}
+                int y = ((uint8_t*)b->gi[i].data)[j];
+                if ( ploidy==1 )
+                {
+                    if ( y>>7&1 )
+                        kputc('.', 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;
@@ -299,6 +323,50 @@ int bcf_append_info(bcf1_t *b, const char *info, int l)
 	return 0;
 }
 
+int remove_tag(char *str, const 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++;        // the tag is first, don't move the delim char
+        len_diff += q-p;
+        if ( ! *q ) { *p = 0; break; }  // the tag was last, no delim follows
+        else
+            memmove(p,q,ori_len-(int)(p-str)-(int)(q-p));  // *q==delim
+    }
+    if ( len_diff==ori_len )
+        str[0]='.', str[1]=0, len_diff--;
+
+    return len_diff;
+}
+
+
+void rm_info(kstring_t *s, const char *key)
+{
+    char *p = s->s; 
+    int n = 0;
+    while ( n<4 )
+    {
+        if ( !*p ) n++;
+        p++;
+    }
+    char *q = p+1; 
+    while ( *q && q-s->s<s->l ) q++;
+
+    int nrm = remove_tag(p, key, ';');
+    if ( nrm )
+        memmove(q-nrm, q, s->s+s->l-q+1);
+    s->l -= nrm;
+}
+
 int bcf_cpy(bcf1_t *r, const bcf1_t *b)
 {
 	char *t1 = r->str;