diff tests/artificial-nofilt.csv.out @ 8:411adeff1eec draft

Handle "." sample columns, update tests to work with BIAS column.
author nick
date Tue, 23 Aug 2016 02:30:56 -0400
parents 31361191d2d2
children 6cc488e11544
line wrap: on
line diff
--- a/tests/artificial-nofilt.csv.out	Wed Dec 09 11:37:02 2015 -0500
+++ b/tests/artificial-nofilt.csv.out	Tue Aug 23 02:30:56 2016 -0400
@@ -1,27 +1,27 @@
-#SAMPLE	CHR	POS	A	C	G	T	CVRG	ALLELES	MAJOR	MINOR	MINOR.FREQ.PERC.
-THYROID	chr1	0	30	0	0	0	30	1	A	.	0.0
-THYROID	chr1	10	30	0	2	0	32	2	A	G	0.0625
-THYROID	chr1	20	31	0	1	0	32	0	A	G	0.03125
-THYROID	chr1	30	21	0	4	0	25	2	A	G	0.16
-THYROID	chr1	40	22	0	3	0	25	0	A	G	0.12
-THYROID	chr1	50	3	0	0	0	3	1	A	.	0.0
-THYROID	chr1	60	2	0	2	0	4	2	A	G	0.5
-THYROID	chr1	70	1	0	3	0	4	0	G	A	0.25
-THYROID	chr1	80	104	0	3	0	107	0	A	G	0.02804
-THYROID	chr1	90	100	2	11	0	113	3	A	G	0.09735
-THYROID	chr1	100	100	1	11	0	112	0	A	G	0.09821
-THYROID	chr1	120	0	0	0	0	0	0	.	.	0.0
-THYROID	chr1	130	0	0	2	0	2	1	G	.	0.0
-THYROID	chr1	140	0	0	1	0	1	0	G	.	0.0
-THYROID	chr1	150	0	0	4	0	4	1	G	.	0.0
-THYROID	chr1	160	0	0	3	0	3	0	G	.	0.0
-THYROID	chr1	260	106	0	14	0	120	2	A	G	0.11667
-THYROID	chr1	300	2	0	2	76	80	3	T	G	0.025
-THYROID	chr1	310	12	0	12	76	100	3	T	G	0.12
-THYROID	chr1	320	12	0	12	56	80	3	T	A	0.15
-THYROID	chr1	330	7	0	7	66	80	3	T	G	0.0875
-THYROID	chr1	340	1	0	1	98	100	0	T	G	0.01
-THYROID	chr1	350	11	0	11	78	100	0	T	A	0.11
-THYROID	chr1	400	32	0	8	0	40	2	A	G	0.2
-THYROID	chr1	410	1	0	2	97	100	0	T	G	0.02
-THYROID	chr1	420	104	0	0	0	104	1	A	.	0.0
+#SAMPLE	CHR	POS	A	C	G	T	CVRG	ALLELES	MAJOR	MINOR	MAF	BIAS
+THYROID	chr1	0	30	0	0	0	30	1	A	.	0.0	.
+THYROID	chr1	10	30	0	2	0	32	2	A	G	0.0625	0.0
+THYROID	chr1	20	31	0	1	0	32	0	A	G	0.03125	2.0
+THYROID	chr1	30	21	0	4	0	25	2	A	G	0.16	0.08013
+THYROID	chr1	40	22	0	3	0	25	0	A	G	0.12	1.78571
+THYROID	chr1	50	3	0	0	0	3	1	A	.	0.0	.
+THYROID	chr1	60	2	0	2	0	4	2	A	G	0.5	0.0
+THYROID	chr1	70	1	0	3	0	4	0	G	A	0.25	2.0
+THYROID	chr1	80	104	0	3	0	107	0	A	G	0.02804	1.01905
+THYROID	chr1	90	100	2	11	0	113	3	A	G	0.09735	0.16381
+THYROID	chr1	100	100	1	11	0	112	0	A	G	0.09821	0.16381
+THYROID	chr1	120	0	0	0	0	0	0	.	.	0.0	.
+THYROID	chr1	130	0	0	2	0	2	1	G	.	0.0	.
+THYROID	chr1	140	0	0	1	0	1	0	G	.	0.0	.
+THYROID	chr1	150	0	0	4	0	4	1	G	.	0.0	.
+THYROID	chr1	160	0	0	3	0	3	0	G	.	0.0	.
+THYROID	chr1	260	106	0	14	0	120	2	A	G	0.11667	2.4
+THYROID	chr1	300	2	0	2	76	80	3	T	G	0.025	0.0
+THYROID	chr1	310	12	0	12	76	100	3	T	G	0.12	0.0
+THYROID	chr1	320	12	0	12	56	80	3	T	A	0.15	0.64394
+THYROID	chr1	330	7	0	7	66	80	3	T	G	0.0875	1.06247
+THYROID	chr1	340	1	0	1	98	100	0	T	G	0.01	5.21053
+THYROID	chr1	350	11	0	11	78	100	0	T	A	0.11	1.25352
+THYROID	chr1	400	32	0	8	0	40	2	A	G	0.2	0.0
+THYROID	chr1	410	1	0	2	97	100	0	T	G	0.02	5.5
+THYROID	chr1	420	104	0	0	0	104	1	A	.	0.0	.