Remove all-missing fields from example VCF

Closes sgkit-dev#1197
jeromekelleher · Feb 16, 2024 · adfe9e6 · adfe9e6
1 parent c7db1d0
commit adfe9e6
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Showing 3 changed files with 54 additions and 54 deletions.
diff --git a/sgkit/tests/io/vcf/data/all_fields.vcf b/sgkit/tests/io/vcf/data/all_fields.vcf
@@ -49,20 +49,20 @@
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	s1	s2
 1	1	.	G	A,C	.	PASS	IB0	.	.	.
 1	2	.	A	G,G	.	PASS	II1=126	.	.	.
-1	3	.	A	G,G	.	PASS	II1=.	.	.	.
+1	3	.	A	G,G	.	PASS	.	.	.	.
 1	4	.	T	A,C	.	PASS	II2=459,-140	.	.	.
 1	5	.	T	A,C	.	PASS	II2=.,-140	.	.	.
 1	6	.	T	A,C	.	PASS	II2=459,.	.	.	.
-1	7	.	T	A,C	.	PASS	II2=.,.	.	.	.
+1	7	.	T	A,C	.	PASS	.	.	.	.
 1	8	.	A	A,G	.	PASS	IIA=294,130	.	.	.
 1	9	.	A	A,G	.	PASS	IIA=.,130	.	.	.
 1	10	.	A	A,G	.	PASS	IIA=294,.	.	.	.
-1	11	.	A	A,G	.	PASS	IIA=.,.	.	.	.
+1	11	.	A	A,G	.	PASS	.	.	.	.
 1	12	.	A	A,G	.	PASS	IIR=95,724,44	.	.	.
 1	13	.	A	A,G	.	PASS	IIR=.,724,44	.	.	.
 1	14	.	A	A,G	.	PASS	IIR=95,.,44	.	.	.
 1	15	.	A	A,G	.	PASS	IIR=95,724,.	.	.	.
-1	16	.	A	A,G	.	PASS	IIR=.,.,.	.	.	.
+1	16	.	A	A,G	.	PASS	.	.	.	.
 1	17	.	G	A,G	.	PASS	IID=-879,-534,238,-670,482,-913,396	.	.	.
 1	18	.	G	A,G	.	PASS	IID=.,-534,238,-670,482,-913,396	.	.	.
 1	19	.	G	A,G	.	PASS	IID=-879,.,238,-670,482,-913,396	.	.	.
@@ -71,28 +71,28 @@
 1	22	.	G	A,G	.	PASS	IID=-879,-534,238,-670,.,-913,396	.	.	.
 1	23	.	G	A,G	.	PASS	IID=-879,-534,238,-670,482,.,396	.	.	.
 1	24	.	G	A,G	.	PASS	IID=-879,-534,238,-670,482,-913,.	.	.	.
-1	25	.	G	A,G	.	PASS	IID=.,.,.,.,.,.,.	.	.	.
+1	25	.	G	A,G	.	PASS	.	.	.	.
 1	26	.	G	A,G	.	PASS	IID=-129,687,-870,685	.	.	.
 1	27	.	G	A,G	.	PASS	IID=.,687,-870,685	.	.	.
 1	28	.	G	A,G	.	PASS	IID=-129,.,-870,685	.	.	.
 1	29	.	G	A,G	.	PASS	IID=-129,687,.,685	.	.	.
 1	30	.	G	A,G	.	PASS	IID=-129,687,-870,.	.	.	.
-1	31	.	G	A,G	.	PASS	IID=.,.,.,.	.	.	.
+1	31	.	G	A,G	.	PASS	.	.	.	.
 1	32	.	T	A,T	.	PASS	IF1=-887.177	.	.	.
-1	33	.	T	A,T	.	PASS	IF1=.	.	.	.
+1	33	.	T	A,T	.	PASS	.	.	.	.
 1	34	.	G	C,A	.	PASS	IF2=443.998,877.105	.	.	.
 1	35	.	G	C,A	.	PASS	IF2=.,877.105	.	.	.
 1	36	.	G	C,A	.	PASS	IF2=443.998,.	.	.	.
-1	37	.	G	C,A	.	PASS	IF2=.,.	.	.	.
+1	37	.	G	C,A	.	PASS	.	.	.	.
 1	38	.	T	C,A	.	PASS	IFA=-998.442,984.423	.	.	.
 1	39	.	T	C,A	.	PASS	IFA=.,984.423	.	.	.
 1	40	.	T	C,A	.	PASS	IFA=-998.442,.	.	.	.
-1	41	.	T	C,A	.	PASS	IFA=.,.	.	.	.
+1	41	.	T	C,A	.	PASS	.	.	.	.
 1	42	.	A	T,G	.	PASS	IFR=234.963,223.306,-985.867	.	.	.
 1	43	.	A	T,G	.	PASS	IFR=.,223.306,-985.867	.	.	.
 1	44	.	A	T,G	.	PASS	IFR=234.963,.,-985.867	.	.	.
 1	45	.	A	T,G	.	PASS	IFR=234.963,223.306,.	.	.	.
-1	46	.	A	T,G	.	PASS	IFR=.,.,.	.	.	.
+1	46	.	A	T,G	.	PASS	.	.	.	.
 1	47	.	T	G,G	.	PASS	IFD=-417.542,223.706,-721.012,-415.711,-267.276,-87.86,570.352,-600.652,28.4689	.	.	.
 1	48	.	T	G,G	.	PASS	IFD=.,223.706,-721.012,-415.711,-267.276,-87.86,570.352,-600.652,28.4689	.	.	.
 1	49	.	T	G,G	.	PASS	IFD=-417.542,.,-721.012,-415.711,-267.276,-87.86,570.352,-600.652,28.4689	.	.	.
@@ -103,7 +103,7 @@
 1	54	.	T	G,G	.	PASS	IFD=-417.542,223.706,-721.012,-415.711,-267.276,-87.86,.,-600.652,28.4689	.	.	.
 1	55	.	T	G,G	.	PASS	IFD=-417.542,223.706,-721.012,-415.711,-267.276,-87.86,570.352,.,28.4689	.	.	.
 1	56	.	T	G,G	.	PASS	IFD=-417.542,223.706,-721.012,-415.711,-267.276,-87.86,570.352,-600.652,.	.	.	.
-1	57	.	T	G,G	.	PASS	IFD=.,.,.,.,.,.,.,.,.	.	.	.
+1	57	.	T	G,G	.	PASS	.	.	.	.
 1	58	.	T	G,G	.	PASS	IFD=-907.099,215.09,-658.952,-869.897,897.771,931.264,616.795,-390.772,-804.656	.	.	.
 1	59	.	T	G,G	.	PASS	IFD=.,215.09,-658.952,-869.897,897.771,931.264,616.795,-390.772,-804.656	.	.	.
 1	60	.	T	G,G	.	PASS	IFD=-907.099,.,-658.952,-869.897,897.771,931.264,616.795,-390.772,-804.656	.	.	.
@@ -114,28 +114,28 @@
 1	65	.	T	G,G	.	PASS	IFD=-907.099,215.09,-658.952,-869.897,897.771,931.264,.,-390.772,-804.656	.	.	.
 1	66	.	T	G,G	.	PASS	IFD=-907.099,215.09,-658.952,-869.897,897.771,931.264,616.795,.,-804.656	.	.	.
 1	67	.	T	G,G	.	PASS	IFD=-907.099,215.09,-658.952,-869.897,897.771,931.264,616.795,-390.772,.	.	.	.
-1	68	.	T	G,G	.	PASS	IFD=.,.,.,.,.,.,.,.,.	.	.	.
+1	68	.	T	G,G	.	PASS	.	.	.	.
 1	69	.	T	C,G	.	PASS	IC1=f	.	.	.
-1	70	.	T	C,G	.	PASS	IC1=.	.	.	.
+1	70	.	T	C,G	.	PASS	.	.	.	.
 1	71	.	G	T,G	.	PASS	IC2=e,a	.	.	.
 1	72	.	G	T,G	.	PASS	IC2=.,a	.	.	.
 1	73	.	G	T,G	.	PASS	IC2=e,.	.	.	.
-1	74	.	G	T,G	.	PASS	IC2=.,.	.	.	.
+1	74	.	G	T,G	.	PASS	.	.	.	.
 1	75	.	A	C,A	.	PASS	ICA=b,a	.	.	.
 1	76	.	A	C,A	.	PASS	ICA=.,a	.	.	.
 1	77	.	A	C,A	.	PASS	ICA=b,.	.	.	.
-1	78	.	A	C,A	.	PASS	ICA=.,.	.	.	.
+1	78	.	A	C,A	.	PASS	.	.	.	.
 1	79	.	C	G,C	.	PASS	ICR=c,b,b	.	.	.
 1	80	.	C	G,C	.	PASS	ICR=.,b,b	.	.	.
 1	81	.	C	G,C	.	PASS	ICR=c,.,b	.	.	.
 1	82	.	C	G,C	.	PASS	ICR=c,b,.	.	.	.
-1	83	.	C	G,C	.	PASS	ICR=.,.,.	.	.	.
+1	83	.	C	G,C	.	PASS	.	.	.	.
 1	84	.	T	G,G	.	PASS	ICD=b,f,b,c	.	.	.
 1	85	.	T	G,G	.	PASS	ICD=.,f,b,c	.	.	.
 1	86	.	T	G,G	.	PASS	ICD=b,.,b,c	.	.	.
 1	87	.	T	G,G	.	PASS	ICD=b,f,.,c	.	.	.
 1	88	.	T	G,G	.	PASS	ICD=b,f,b,.	.	.	.
-1	89	.	T	G,G	.	PASS	ICD=.,.,.,.	.	.	.
+1	89	.	T	G,G	.	PASS	.	.	.	.
 1	90	.	T	G,G	.	PASS	ICD=g,e,d,e,f,f,b	.	.	.
 1	91	.	T	G,G	.	PASS	ICD=.,e,d,e,f,f,b	.	.	.
 1	92	.	T	G,G	.	PASS	ICD=g,.,d,e,f,f,b	.	.	.
@@ -144,22 +144,22 @@
 1	95	.	T	G,G	.	PASS	ICD=g,e,d,e,.,f,b	.	.	.
 1	96	.	T	G,G	.	PASS	ICD=g,e,d,e,f,.,b	.	.	.
 1	97	.	T	G,G	.	PASS	ICD=g,e,d,e,f,f,.	.	.	.
-1	98	.	T	G,G	.	PASS	ICD=.,.,.,.,.,.,.	.	.	.
+1	98	.	T	G,G	.	PASS	.	.	.	.
 1	99	.	A	C,C	.	PASS	IS1=bc	.	.	.
-1	100	.	A	C,C	.	PASS	IS1=.	.	.	.
+1	100	.	A	C,C	.	PASS	.	.	.	.
 1	101	.	T	T,C	.	PASS	IS2=hij,d	.	.	.
 1	102	.	T	T,C	.	PASS	IS2=.,d	.	.	.
 1	103	.	T	T,C	.	PASS	IS2=hij,.	.	.	.
-1	104	.	T	T,C	.	PASS	IS2=.,.	.	.	.
+1	104	.	T	T,C	.	PASS	.	.	.	.
 1	105	.	T	C,C	.	PASS	ISA=bc,efg	.	.	.
 1	106	.	T	C,C	.	PASS	ISA=.,efg	.	.	.
 1	107	.	T	C,C	.	PASS	ISA=bc,.	.	.	.
-1	108	.	T	C,C	.	PASS	ISA=.,.	.	.	.
+1	108	.	T	C,C	.	PASS	.	.	.	.
 1	109	.	C	G,T	.	PASS	ISR=d,bc,op	.	.	.
 1	110	.	C	G,T	.	PASS	ISR=.,bc,op	.	.	.
 1	111	.	C	G,T	.	PASS	ISR=d,.,op	.	.	.
 1	112	.	C	G,T	.	PASS	ISR=d,bc,.	.	.	.
-1	113	.	C	G,T	.	PASS	ISR=.,.,.	.	.	.
+1	113	.	C	G,T	.	PASS	.	.	.	.
 1	114	.	G	A,A	.	PASS	ISD=ab,hij,klmn,d,ab,d,op,efg	.	.	.
 1	115	.	G	A,A	.	PASS	ISD=.,hij,klmn,d,ab,d,op,efg	.	.	.
 1	116	.	G	A,A	.	PASS	ISD=ab,.,klmn,d,ab,d,op,efg	.	.	.
@@ -169,89 +169,89 @@
 1	120	.	G	A,A	.	PASS	ISD=ab,hij,klmn,d,ab,.,op,efg	.	.	.
 1	121	.	G	A,A	.	PASS	ISD=ab,hij,klmn,d,ab,d,.,efg	.	.	.
 1	122	.	G	A,A	.	PASS	ISD=ab,hij,klmn,d,ab,d,op,.	.	.	.
-1	123	.	G	A,A	.	PASS	ISD=.,.,.,.,.,.,.,.	.	.	.
+1	123	.	G	A,A	.	PASS	.	.	.	.
 1	124	.	G	A,A	.	PASS	ISD=op,op,ab	.	.	.
 1	125	.	G	A,A	.	PASS	ISD=.,op,ab	.	.	.
 1	126	.	G	A,A	.	PASS	ISD=op,.,ab	.	.	.
 1	127	.	G	A,A	.	PASS	ISD=op,op,.	.	.	.
-1	128	.	G	A,A	.	PASS	ISD=.,.,.	.	.	.
+1	128	.	G	A,A	.	PASS	.	.	.	.
 2	129	.	G	G,G	.	PASS	.	FI1	-795	.
 2	130	.	C	G,A	.	PASS	.	FI2	104,955	.,955
-2	131	.	C	G,A	.	PASS	.	FI2	104,.	.,.
+2	131	.	C	G,A	.	PASS	.	FI2	104,.	.
 2	132	.	C	C,T	.	PASS	.	FIA	585,895	.,895
-2	133	.	C	C,T	.	PASS	.	FIA	585,.	.,.
+2	133	.	C	C,T	.	PASS	.	FIA	585,.	.
 2	134	.	T	C,G	.	PASS	.	FIR	411,25,21	.,25,21
 2	135	.	T	C,G	.	PASS	.	FIR	411,.,21	411,25,.
-2	136	.	T	C,G	.	PASS	.	FIR	.,.,.	.,.,.
+2	136	.	T	C,G	.	PASS	.	FIR	.	.
 2	137	.	A	T,T	.	PASS	.	FIG	413,-435,129,795,845,500	.,-435,129,795,845,500
 2	138	.	A	T,T	.	PASS	.	FIG	413,.,129,795,845,500	413,-435,.,795,845,500
 2	139	.	A	T,T	.	PASS	.	FIG	413,-435,129,.,845,500	413,-435,129,795,.,500
-2	140	.	A	T,T	.	PASS	.	FIG	413,-435,129,795,845,.	.,.,.,.,.,.
+2	140	.	A	T,T	.	PASS	.	FIG	413,-435,129,795,845,.	.
 2	141	.	C	G,G	.	PASS	.	FID	-271,579	.,579
-2	142	.	C	G,G	.	PASS	.	FID	-271,.	.,.
+2	142	.	C	G,G	.	PASS	.	FID	-271,.	.
 2	143	.	C	G,G	.	PASS	.	FID	-799,981	.,981
-2	144	.	C	G,G	.	PASS	.	FID	-799,.	.,.
+2	144	.	C	G,G	.	PASS	.	FID	-799,.	.
 2	145	.	A	T,G	.	PASS	.	FF1	853.318	.
 2	146	.	T	G,A	.	PASS	.	FF2	454.544,-346.918	.,-346.918
-2	147	.	T	G,A	.	PASS	.	FF2	454.544,.	.,.
+2	147	.	T	G,A	.	PASS	.	FF2	454.544,.	.
 2	148	.	C	A,T	.	PASS	.	FFA	140.888,41.6685	.,41.6685
-2	149	.	C	A,T	.	PASS	.	FFA	140.888,.	.,.
+2	149	.	C	A,T	.	PASS	.	FFA	140.888,.	.
 2	150	.	T	T,C	.	PASS	.	FFR	922.344,689.068,494.64	.,689.068,494.64
 2	151	.	T	T,C	.	PASS	.	FFR	922.344,.,494.64	922.344,689.068,.
-2	152	.	T	T,C	.	PASS	.	FFR	.,.,.	.,.,.
+2	152	.	T	T,C	.	PASS	.	FFR	.	.
 2	153	.	A	T,T	.	PASS	.	FFG	79.3843,173.502,930.511,214.068,-448.002,-407.453	.,173.502,930.511,214.068,-448.002,-407.453
 2	154	.	A	T,T	.	PASS	.	FFG	79.3843,.,930.511,214.068,-448.002,-407.453	79.3843,173.502,.,214.068,-448.002,-407.453
 2	155	.	A	T,T	.	PASS	.	FFG	79.3843,173.502,930.511,.,-448.002,-407.453	79.3843,173.502,930.511,214.068,.,-407.453
-2	156	.	A	T,T	.	PASS	.	FFG	79.3843,173.502,930.511,214.068,-448.002,.	.,.,.,.,.,.
+2	156	.	A	T,T	.	PASS	.	FFG	79.3843,173.502,930.511,214.068,-448.002,.	.
 2	157	.	A	C,A	.	PASS	.	FFD	-968.727	.
 2	158	.	A	C,A	.	PASS	.	FFD	544.49,-602.569,-988.956,630.923,413.715,458.014,542.541,-851.911,-283.069	.,-602.569,-988.956,630.923,413.715,458.014,542.541,-851.911,-283.069
 2	159	.	A	C,A	.	PASS	.	FFD	544.49,.,-988.956,630.923,413.715,458.014,542.541,-851.911,-283.069	544.49,-602.569,.,630.923,413.715,458.014,542.541,-851.911,-283.069
 2	160	.	A	C,A	.	PASS	.	FFD	544.49,-602.569,-988.956,.,413.715,458.014,542.541,-851.911,-283.069	544.49,-602.569,-988.956,630.923,.,458.014,542.541,-851.911,-283.069
 2	161	.	A	C,A	.	PASS	.	FFD	544.49,-602.569,-988.956,630.923,413.715,.,542.541,-851.911,-283.069	544.49,-602.569,-988.956,630.923,413.715,458.014,.,-851.911,-283.069
 2	162	.	A	C,A	.	PASS	.	FFD	544.49,-602.569,-988.956,630.923,413.715,458.014,542.541,.,-283.069	544.49,-602.569,-988.956,630.923,413.715,458.014,542.541,-851.911,.
-2	163	.	A	C,A	.	PASS	.	FFD	.,.,.,.,.,.,.,.,.	.,.,.,.,.,.,.,.,.
+2	163	.	A	C,A	.	PASS	.	FFD	.	.
 2	164	.	T	T,A	.	PASS	.	FC1	d	.
 2	165	.	G	C,T	.	PASS	.	FC2	c,b	.,b
-2	166	.	G	C,T	.	PASS	.	FC2	c,.	.,.
+2	166	.	G	C,T	.	PASS	.	FC2	c,.	.
 2	167	.	G	G,A	.	PASS	.	FCA	c,g	.,g
-2	168	.	G	G,A	.	PASS	.	FCA	c,.	.,.
+2	168	.	G	G,A	.	PASS	.	FCA	c,.	.
 2	169	.	G	C,G	.	PASS	.	FCR	a,b,c	.,b,c
 2	170	.	G	C,G	.	PASS	.	FCR	a,.,c	a,b,.
-2	171	.	G	C,G	.	PASS	.	FCR	.,.,.	.,.,.
+2	171	.	G	C,G	.	PASS	.	FCR	.	.
 2	172	.	G	A,A	.	PASS	.	FCG	a,e,b,g,g,a	.,e,b,g,g,a
 2	173	.	G	A,A	.	PASS	.	FCG	a,.,b,g,g,a	a,e,.,g,g,a
 2	174	.	G	A,A	.	PASS	.	FCG	a,e,b,.,g,a	a,e,b,g,.,a
-2	175	.	G	A,A	.	PASS	.	FCG	a,e,b,g,g,.	.,.,.,.,.,.
+2	175	.	G	A,A	.	PASS	.	FCG	a,e,b,g,g,.	.
 2	176	.	A	G,A	.	PASS	.	FCD	a,g,d,d,f,f,b,a,d	.,g,d,d,f,f,b,a,d
 2	177	.	A	G,A	.	PASS	.	FCD	a,.,d,d,f,f,b,a,d	a,g,.,d,f,f,b,a,d
 2	178	.	A	G,A	.	PASS	.	FCD	a,g,d,.,f,f,b,a,d	a,g,d,d,.,f,b,a,d
 2	179	.	A	G,A	.	PASS	.	FCD	a,g,d,d,f,.,b,a,d	a,g,d,d,f,f,.,a,d
 2	180	.	A	G,A	.	PASS	.	FCD	a,g,d,d,f,f,b,.,d	a,g,d,d,f,f,b,a,.
-2	181	.	A	G,A	.	PASS	.	FCD	.,.,.,.,.,.,.,.,.	c,d,f,e,g,a,c
+2	181	.	A	G,A	.	PASS	.	FCD	.	c,d,f,e,g,a,c
 2	182	.	A	G,A	.	PASS	.	FCD	.,d,f,e,g,a,c	c,.,f,e,g,a,c
 2	183	.	A	G,A	.	PASS	.	FCD	c,d,.,e,g,a,c	c,d,f,.,g,a,c
 2	184	.	A	G,A	.	PASS	.	FCD	c,d,f,e,.,a,c	c,d,f,e,g,.,c
-2	185	.	A	G,A	.	PASS	.	FCD	c,d,f,e,g,a,.	.,.,.,.,.,.,.
+2	185	.	A	G,A	.	PASS	.	FCD	c,d,f,e,g,a,.	.
 2	186	.	C	T,A	.	PASS	.	FS1	bc	.
 2	187	.	C	C,C	.	PASS	.	FS2	bc,op	.,op
-2	188	.	C	C,C	.	PASS	.	FS2	bc,.	.,.
+2	188	.	C	C,C	.	PASS	.	FS2	bc,.	.
 2	189	.	C	T,G	.	PASS	.	FSA	ab,op	.,op
-2	190	.	C	T,G	.	PASS	.	FSA	ab,.	.,.
+2	190	.	C	T,G	.	PASS	.	FSA	ab,.	.
 2	191	.	T	T,T	.	PASS	.	FSR	klmn,bc,efg	.,bc,efg
 2	192	.	T	T,T	.	PASS	.	FSR	klmn,.,efg	klmn,bc,.
-2	193	.	T	T,T	.	PASS	.	FSR	.,.,.	.,.,.
+2	193	.	T	T,T	.	PASS	.	FSR	.	.
 2	194	.	A	C,A	.	PASS	.	FSG	d,op,bc,klmn,efg,d	.,op,bc,klmn,efg,d
 2	195	.	A	C,A	.	PASS	.	FSG	d,.,bc,klmn,efg,d	d,op,.,klmn,efg,d
 2	196	.	A	C,A	.	PASS	.	FSG	d,op,bc,.,efg,d	d,op,bc,klmn,.,d
-2	197	.	A	C,A	.	PASS	.	FSG	d,op,bc,klmn,efg,.	.,.,.,.,.,.
+2	197	.	A	C,A	.	PASS	.	FSG	d,op,bc,klmn,efg,.	.
 2	198	.	T	T,G	.	PASS	.	FSD	klmn,bc,d,op,hij,efg,klmn,ab,hij	.,bc,d,op,hij,efg,klmn,ab,hij
 2	199	.	T	T,G	.	PASS	.	FSD	klmn,.,d,op,hij,efg,klmn,ab,hij	klmn,bc,.,op,hij,efg,klmn,ab,hij
 2	200	.	T	T,G	.	PASS	.	FSD	klmn,bc,d,.,hij,efg,klmn,ab,hij	klmn,bc,d,op,.,efg,klmn,ab,hij
 2	201	.	T	T,G	.	PASS	.	FSD	klmn,bc,d,op,hij,.,klmn,ab,hij	klmn,bc,d,op,hij,efg,.,ab,hij
 2	202	.	T	T,G	.	PASS	.	FSD	klmn,bc,d,op,hij,efg,klmn,.,hij	klmn,bc,d,op,hij,efg,klmn,ab,.
-2	203	.	T	T,G	.	PASS	.	FSD	.,.,.,.,.,.,.,.,.	efg,klmn,bc,op,ab,bc,hij,hij
+2	203	.	T	T,G	.	PASS	.	FSD	.	efg,klmn,bc,op,ab,bc,hij,hij
 2	204	.	T	T,G	.	PASS	.	FSD	.,klmn,bc,op,ab,bc,hij,hij	efg,.,bc,op,ab,bc,hij,hij
 2	205	.	T	T,G	.	PASS	.	FSD	efg,klmn,.,op,ab,bc,hij,hij	efg,klmn,bc,.,ab,bc,hij,hij
 2	206	.	T	T,G	.	PASS	.	FSD	efg,klmn,bc,op,.,bc,hij,hij	efg,klmn,bc,op,ab,.,hij,hij
 2	207	.	T	T,G	.	PASS	.	FSD	efg,klmn,bc,op,ab,bc,.,hij	efg,klmn,bc,op,ab,bc,hij,.
-2	208	.	T	T,G	.	PASS	.	FSD	.,.,.,.,.,.,.,.	.,.,.,.,.,.,.,.
+2	208	.	T	T,G	.	PASS	.	FSD	.	.
diff --git a/sgkit/tests/io/vcf/test_vcf_roundtrip.py b/sgkit/tests/io/vcf/test_vcf_roundtrip.py
@@ -31,9 +31,7 @@
             },
             True,
         ),
-        # Temporarily disabling this all_fields test while resolving missing data issue
-        # https://github.com/pystatgen/sgkit/issues/1197
-        # ("all_fields.vcf", None, True),
+        ("all_fields.vcf", None, True),
         ("CEUTrio.20.21.gatk3.4.g.vcf.bgz", None, True),
         # don't generate header to avoid https://github.com/pydata/xarray/issues/7328
         ("Homo_sapiens_assembly38.headerOnly.vcf.gz", None, False),

diff --git a/sgkit/tests/io/vcf/vcf_generator.py b/sgkit/tests/io/vcf/vcf_generator.py
@@ -70,15 +70,15 @@ def generate_values(self, alt_alleles):
             n = generate_number(self.vcf_number, alt_alleles)
             data = generate_data(self.vcf_type, n)
             val = ",".join([str(x) for x in data])
+            assert val != "."
             yield f"{val}"
             for i in range(n):
                 data_str = [str(x) for x in data]
                 data_str[i] = "."  # missing
                 val = ",".join(data_str)
-                yield f"{val}"
+                yield f"{val}" if val != "." else None
             if n > 1:
-                val = ",".join(["."] * n)  # all missing
-                yield f"{val}"
+                yield None  # all missing
 
 
 def generate_header(info_fields, format_fields, vcf_samples):
@@ -154,7 +154,9 @@ def generate_vcf(output, seed=42):
                 pos = pos + 1
                 ref = alleles[0]
                 alt = alleles[1:]
-                info = {info_field.name: val}
+                info = {}
+                if val is not None:
+                    info = {info_field.name: val}
                 samples: List[Dict[str, Any]] = [{}] * len(vcf_samples)
 
                 variant = VcfVariant(