Update test-01

Author: reedacartwright

test/test-01.bash

@@ -1,11 +1,14 @@
 #!/bin/bash
+#
+# library(rmutil)
+# f = function(n,a,b) dbetabinom(0:n,n,a/(a+b),a+b)
 
 echo "Running Integration Test: unfolded+tagged ..."
 
-SOFOS=$1
+SOFOS="${1:-../sofos}"
 VCF=test-default.vcf
 
-output=$(${SOFOS} -q -a 0.1 -b 1 -n 10 -u -t ${VCF}) 
+output=$(${SOFOS} -q -a 0.1 -b 1 -n 10 -u -t ${VCF})
 
 hnum=$(echo "${output}" | grep '^#' | wc -l)
 if [[ 10 -ne "${hnum}" ]]; then
@@ -19,17 +22,17 @@ if [[ $header != "Number,Prior,Observed,Posterior" ]]; then
 fi
 
 # Check posterior
-expected="0.341830374360738
-0.250675607864541
-0.169206035308565
-0.107597683991088
-0.0643344485530045
-0.0357933477403989
-0.018194951768036
-0.00820216873352734
-0.00311426094101116
-0.000899675382958782
-0.000151445356131395"
+expected="0.649602923876743
+0.476864186047936
+0.323085024970344
+0.207787973205851
+0.128175439263581
+0.0772737404468384
+0.0475690799391035
+0.0320738639692642
+0.0246226484295746
+0.0198606972724853
+0.0130844225782785"
 
 echo "${output}" | grep -v '^#' | awk -F, 'NR>1 {print $4}' \
 	| paste -d, - <(echo "${expected}") \
@@ -40,17 +43,17 @@ if [[ $? -ne 0 ]]; then
 fi
 
 # Check prior
-expected="0.751621782268415
-0.0751621782268415
-0.0413391980247626
-0.0289374386173338
-0.0224265149284337
-0.0183897422413156
-0.0156312809051183
-0.0136215447887459
-0.012089121000012
-0.0108802089000108
-0.00990099009900991"
+expected="1.50324356453683
+0.150324356453683
+0.0826783960495252
+0.0578748772346676
+0.0448530298568674
+0.0367794844826313
+0.0312625618102366
+0.0272430895774919
+0.0241782420000241
+0.0217604178000216
+0.0198019801980198"
 
 echo "${output}" | grep -v '^#' | awk -F, 'NR>1 {print $2}' \
 	| paste -d, - <(echo "${expected}") \
@@ -63,12 +66,13 @@ fi
 # Check obs
 expected="0
 0
-1
+1.9
 0
 0
 0
 0
 0
+0.1
 0
 0"
 

test/test-default.vcf

@@ -8,4 +8,5 @@
 ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Posteriors">
 ##contig=<ID=1,length=10000>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C
-1	1	.	A	C	30	PASS	AA=A;AN=6;AC=1	GT:GP	0/1:0,1,0	0/0:1,0,0	0/0:0,0,1
+1	1	.	A	C	30	PASS	AA=A;AN=6;AC=1	GT	0/1	0/0	0/0
+1	2	.	A	C	30	PASS	AA=C;AAQ=10	GT:GP	0/1	1/1	1/1