r281: optional: "." in a multi-allelic GT

atomic.c

@@ -246,10 +246,11 @@ const bcf_atom_t *bcf_atom_read(bcf_atombuf_t *buf)
 	}
 }
 
-void bcf_atom2bcf(const bcf_atom_t *a, bcf1_t *b, int write_M, int id_GT)
+void bcf_atom2bcf2(const bcf_atom_t *a, bcf1_t *b, int write_M, int id_GT, int use_missing)
 {
 	static uint8_t conv[4] = { 1<<1, 2<<1, 0<<1, 3<<1 };
 	static uint8_t conv_no_M[4] = { 1<<1, 2<<1, 0<<1, 1<<1 };
+	static uint8_t conv_no_M_missing[4] = { 1<<1, 2<<1, 0<<1, 0<<1 };
 	b->rid = a->rid, b->pos = a->pos, b->rlen = a->rlen;
 	b->qual = 0, b->n_info = b->n_fmt = b->n_sample = 0;
 	b->n_allele = write_M && a->has_multi? 3 : 2;
@@ -271,9 +272,17 @@ void bcf_atom2bcf(const bcf_atom_t *a, bcf1_t *b, int write_M, int id_GT)
 			for (i = 0; i < b->n_sample<<1; ++i)
 				b->indiv.s[b->indiv.l++] = conv[a->gt[i]] | a->phased;
 		} else {
-			for (i = 0; i < b->n_sample<<1; ++i)
-				b->indiv.s[b->indiv.l++] = conv_no_M[a->gt[i]] | a->phased;
+			if (use_missing)
+				for (i = 0; i < b->n_sample<<1; ++i)
+					b->indiv.s[b->indiv.l++] = conv_no_M_missing[a->gt[i]] | a->phased;
+			else
+				for (i = 0; i < b->n_sample<<1; ++i)
+					b->indiv.s[b->indiv.l++] = conv_no_M[a->gt[i]] | a->phased;
 		}
 		b->indiv.s[b->indiv.l] = 0;
 	}
 }
+
+void bcf_atom2bcf(const bcf_atom_t *a, bcf1_t *b, int write_M, int id_GT)
+{
+}

atomic.h

@@ -29,6 +29,7 @@ void bcf_atomize(const bcf_hdr_t *h, bcf1_t *b, bcf_atom_v *a);
 bcf_atombuf_t *bcf_atombuf_init(htsFile *in, int keep_flt);
 void bcf_atombuf_destroy(bcf_atombuf_t *buf);
 const bcf_atom_t *bcf_atom_read(bcf_atombuf_t *buf);
+void bcf_atom2bcf2(const bcf_atom_t *a, bcf1_t *b, int write_M, int id_GT, int use_missing);
 void bcf_atom2bcf(const bcf_atom_t *a, bcf1_t *b, int write_M, int id_GT);
 void bcf_atom_print(const bcf_hdr_t *h, int n, const bcf_atom_t *aa);
 

import.c

@@ -134,26 +134,28 @@ int main_bcfidx(int argc, char *argv[])
 
 int main_atomize(int argc, char *argv[])
 {
-	int c, vcf_in = 0, bcf_out = 0, write_M = 0, id_GT = -1;
+	int c, vcf_in = 0, bcf_out = 0, write_M = 0, id_GT = -1, use_missing = 0;
 	char moder[8], modew[8], *fn_ref = 0;
 	htsFile *in, *out;
 	bcf_atombuf_t *ab;
 	const bcf_atom_t *a;
 	bcf1_t *b;
 
-	while ((c = getopt(argc, argv, "bSMt:")) >= 0) {
+	while ((c = getopt(argc, argv, "mbSMt:")) >= 0) {
 		if (c == 'S') vcf_in = 1;
 		else if (c == 't') vcf_in = 1, fn_ref = optarg;
 		else if (c == 'b') bcf_out = 1;
 		else if (c == 'M') write_M = 1;
+		else if (c == 'm') use_missing = 1;
 	}
 	if (optind == argc) {
 		fprintf(stderr, "Usage: bgt atomize [options] <in.bcf>|<in.vcf>\n");
 		fprintf(stderr, "Options:\n");
 		fprintf(stderr, "  -b       BCF output\n");
 		fprintf(stderr, "  -S       VCF input\n");
 		fprintf(stderr, "  -t FILE  list of contig names and lengths (force -S)\n");
-		fprintf(stderr, "  -M       use <M> symbolic allele\n");
+		fprintf(stderr, "  -M       use <M> at a multi-allelic site (override -m)\n");
+		fprintf(stderr, "  -m       use . at a multi-allelic genotype\n");
 		return 1;
 	}
 
@@ -176,7 +178,7 @@ int main_atomize(int argc, char *argv[])
 
 	b = bcf_init1();
 	while ((a = bcf_atom_read(ab)) != 0) {
-		bcf_atom2bcf(a, b, write_M, id_GT);
+		bcf_atom2bcf2(a, b, write_M, id_GT, use_missing);
 		vcf_write1(out, ab->h, b);
 	}
 	bcf_destroy1(b);

main.c

@@ -3,7 +3,7 @@
 #include <string.h>
 #include <ctype.h>
 
-#define BGT_VERSION "1.0-r280-dirty"
+#define BGT_VERSION "1.0-r281-dirty"
 
 int main_import(int argc, char *argv[]);
 int main_view(int argc, char *argv[]);