X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcf.c;h=0524408da6cf29f4deb6cee09c69d3dce61c4841;hb=ccb7838cb53bf0ca6917a77f7991d940057c12db;hp=b749847d2fc1ce7ca5e5cea755258cdb570a8358;hpb=8af173e8da2ad28aadde5e58ece84d9c448cfe5f;p=samtools.git

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index b749847..0524408 100644
--- a/bcftools/bcf.c
+++ b/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;
 }
 
@@ -103,8 +100,14 @@ int bcf_sync(bcf1_t *b)
 	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;
+	for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
+		if (*p == 0 && p+1 != b->str + b->l_str) {
+			if (n == 5) {
+				++n;
+				break;
+			} else tmp[n++] = p + 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;
@@ -134,12 +137,12 @@ 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].fmt == bcf_str2int("SP", 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("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;
 		}
@@ -227,7 +230,31 @@ 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) {
+
+        // Determine GT with maximum PL (multiple ALT sites only)
+        int imax=-1;
+        if ( iPL!=-1 ) {
+            uint8_t *d = (uint8_t*)b->gi[iPL].data + j * x;
+            int k,identical=1;
+            imax=0;
+            for (k=1; k<x; k++)
+            {
+                if ( identical && d[k]!=d[k-1] ) identical = 0;
+                if ( d[k]<d[imax] ) imax = k;
+            }
+            // If all lks are identical, leave GT untouched
+            if ( identical ) imax = -1;
+        }
 		kputc('\t', s);
 		for (i = 0; i < b->n_gi; ++i) {
 			if (i) kputc(':', s);
@@ -238,19 +265,37 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
 					if (k > 0) kputc(',', s);
 					kputw(d[k], s);
 				}
-			} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+			} 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) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+			} 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 ( y>>7&1 )
+                    kputsn("./.", 3, s);
+                else if ( imax==-1 )
+                {
+                    kputc('0' + (y>>3&7), s);
+                    kputc("/|"[y>>6&1], s);
+                    kputc('0' + (y&7), s);
+                }
+                else
+                {
+                    // Arguably, the while loop will be faster than two sqrts
+                    int n = 0;
+                    int row = 1;
+                    while ( n<imax )
+                    {
+                        row++;
+                        n += row;
+                    }
+                    row--;
+                    kputw(imax-n+row, s);
+                    kputc("/|"[y>>6&1], s);
+                    kputw(row, s);
+                }
 			} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
 				float *d = (float*)b->gi[i].data + j * x;
 				int k;
@@ -259,7 +304,7 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
 					if (k > 0) kputc(',', s);
 					ksprintf(s, "%.2f", d[k]);
 				}
-			}
+			} else kputc('.', s); // custom fields
 		}
 	}
 }