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19928: Fix test cases. 19928-vcf-converter
authorTom Clegg <tom@curii.com>
Wed, 10 Apr 2024 21:04:06 +0000 (17:04 -0400)
committerTom Clegg <tom@curii.com>
Wed, 10 Apr 2024 21:04:06 +0000 (17:04 -0400)
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

gvcf2vcfbed/testdata/converterSuite.TestIndel.txt patch | blob | history
gvcf2vcfbed/testdata/converterSuite.TestNoVariants.txt patch | blob | history

diff --git a/gvcf2vcfbed/testdata/converterSuite.TestIndel.txt b/gvcf2vcfbed/testdata/converterSuite.TestIndel.txt
index d3c1d220fa437e91710203c632d48a41a1509668..50cca4460f1af0090a6f5e7b53deabec238b4844 100644 (file)
--- a/gvcf2vcfbed/testdata/converterSuite.TestIndel.txt
+++ b/gvcf2vcfbed/testdata/converterSuite.TestIndel.txt
@@ -9,8 +9,7 @@ chr22   10516114        .       G       A,<NON_REF>     220.77  .       BaseQRankSum=-0.567;ClippingRankSum=-0.3
 chr22  10516115        .       T       <NON_REF>       .       .       END=10516115    GT:DP:GQ:MIN_DP:PL      0/0:36:87:36:0,87,1305
 chr22  10516116        .       A       <NON_REF>       .       .       END=10516116    GT:DP:GQ:MIN_DP:PL      0/0:36:73:36:0,73,1162
 chr22  10516117        .       T       <NON_REF>       .       .       END=10516121    GT:DP:GQ:MIN_DP:PL      0/0:35:87:34:0,87,1305
-chr22  10516122        .       A       <NON_REF>       .       .       END=10516149    GT:DP:GQ:MIN_DP:PL      0/0:40:90:36:0,90,1350
-chr22  10516150        .       GTA     G,<NON_REF>     198.73  .       BaseQRankSum=-0.073;ClippingRankSum=-1.059;DP=38;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQ0=0;MQRankSum=-4.384;RAW_MQ=119912.00;ReadPosRankSum=-0.694      GT:AD:DP:GQ:PL:SB       0/1:27,9,0:36:99:236,0,921,318,948,1266:12,15,4,5
+chr22  10516122        .       A       <NON_REF>       .       .       END=10516152    GT:DP:GQ:MIN_DP:PL      0/0:40:90:36:0,90,1350
 chr22  10516153        .       T       <NON_REF>       .       .       END=10516153    GT:DP:GQ:MIN_DP:PL      0/0:41:0:41:0,0,800
 chr22  10516154        .       A       <NON_REF>       .       .       END=10516279    GT:DP:GQ:MIN_DP:PL      0/0:47:99:34:0,99,1272
 chr22  10516280        .       A       <NON_REF>       .       .       END=10516289    GT:DP:GQ:MIN_DP:PL      0/0:34:96:34:0,96,1440
@@ -21,9 +20,7 @@ chr22 10516299        .       A       <NON_REF>       .       .       END=10516312    GT:DP:GQ:MIN_DP:PL      0/0:33:90:31:0,
 chr22  10516313        .       C       <NON_REF>       .       .       END=10516314    GT:DP:GQ:MIN_DP:PL      0/0:31:87:31:0,87,1305
 chr22  10516315        .       T       <NON_REF>       .       .       END=10516318    GT:DP:GQ:MIN_DP:PL      0/0:30:78:30:0,78,1170
 chr22  10516319        .       T       <NON_REF>       .       .       END=10516324    GT:DP:GQ:MIN_DP:PL      0/0:30:60:29:0,60,900
-chr22  10516325        .       T       <NON_REF>       .       .       END=10516332    GT:DP:GQ:MIN_DP:PL      0/0:26:54:21:0,54,810
-chr22  10516333        .       G       T,<NON_REF>     12.99   .       BaseQRankSum=0.352;ClippingRankSum=0.151;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQ0=0;MQRankSum=-0.653;RAW_MQ=37658.00;ReadPosRankSum=-2.060 GT:AB:AD:DP:GQ:PL:SB    0/1:0.860:18,3,0:21:41:41,0,5
-21,95,530,625:11,7,0,3
+chr22  10516325        .       T       <NON_REF>       .       .       END=10516333    GT:DP:GQ:MIN_DP:PL      0/0:26:54:21:0,54,810
 chr22  10516334        .       C       <NON_REF>       .       .       END=10516342    GT:DP:GQ:MIN_DP:PL      0/0:18:51:18:0,51,765
 chr22  10516343        .       A       <NON_REF>       .       .       END=10516343    GT:DP:GQ:MIN_DP:PL      0/0:19:54:19:0,54,810
 chr22  10516344        .       T       <NON_REF>       .       .       END=10516344    GT:DP:GQ:MIN_DP:PL      0/0:18:51:18:0,51,765
@@ -54,15 +51,13 @@ chr22       10516420        .       A       <NON_REF>       .       .       END=10516428    GT:DP:GQ:MIN_DP:PL      0/0:14:39:14:0,
 chr22  10516429        .       G       <NON_REF>       .       .       END=10516429    GT:DP:GQ:MIN_DP:PL      0/0:14:36:14:0,36,540
 chr22  10516430        .       A       <NON_REF>       .       .       END=10516430    GT:DP:GQ:MIN_DP:PL      0/0:16:42:16:0,42,630
 chr22  10516431        .       A       <NON_REF>       .       .       END=10516432    GT:DP:GQ:MIN_DP:PL      0/0:16:39:16:0,39,585
-chr22  10516433        .       C       <NON_REF>       .       .       END=10516433    GT:DP:GQ:MIN_DP:PL      0/0:17:42:17:0,42,630
-chr22  10516434        .       A       G,<NON_REF>     103.77  .       BaseQRankSum=-0.182;ClippingRankSum=0.424;DP=16;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQ0=0;MQRankSum=-0.424;RAW_MQ=19613.00;ReadPosRankSum=-0.546        GT:AB:AD:DP:GQ:PGT:PID:PL:SB    0/1:0.750:12,4,0:16:99:0|1:10516434_A_G:132,0,683,168,695,863:4,8,0,4
+chr22  10516433        .       C       <NON_REF>       .       .       END=10516434    GT:DP:GQ:MIN_DP:PL      0/0:17:42:17:0,42,630
 chr22  10516435        .       C       <NON_REF>       .       .       END=10516439    GT:DP:GQ:MIN_DP:PL      0/0:16:42:16:0,42,630
 chr22  10516440        .       T       <NON_REF>       .       .       END=10516442    GT:DP:GQ:MIN_DP:PL      0/0:15:45:15:0,45,522
 chr22  10516443        .       A       <NON_REF>       .       .       END=10516443    GT:DP:GQ:MIN_DP:PL      0/0:16:48:16:0,48,536
 chr22  10516444        .       A       <NON_REF>       .       .       END=10516444    GT:DP:GQ:MIN_DP:PL      0/0:17:51:17:0,51,571
 chr22  10516445        .       T       <NON_REF>       .       .       END=10516445    GT:DP:GQ:MIN_DP:PL      0/0:18:54:18:0,54,626
-chr22  10516446        .       G       <NON_REF>       .       .       END=10516446    GT:DP:GQ:MIN_DP:PL      0/0:19:57:19:0,57,661
-chr22  10516447        .       G       T,<NON_REF>     94.77   .       BaseQRankSum=0.650;ClippingRankSum=-0.150;DP=19;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQ0=0;MQRankSum=-0.650;RAW_MQ=22327.00;ReadPosRankSum=1.150 GT:AB:AD:DP:GQ:PGT:PID:PL:SB    0/1:0.790:15,4,0:19:99:0|1:10516434_A_G:123,0,766,168,778,946:3,12,0,4
+chr22  10516446        .       G       <NON_REF>       .       .       END=10516447    GT:DP:GQ:MIN_DP:PL      0/0:19:57:19:0,57,661
 chr22  10516448        .       T       <NON_REF>       .       .       END=10516452    GT:DP:GQ:MIN_DP:PL      0/0:19:57:19:0,57,651
 chr22  10516453        .       G       <NON_REF>       .       .       END=10516474    GT:DP:GQ:MIN_DP:PL      0/0:22:60:20:0,60,695
 chr22  10516475        .       A       <NON_REF>       .       .       END=10516482    GT:DP:GQ:MIN_DP:PL      0/0:24:72:24:0,72,814
diff --git a/gvcf2vcfbed/testdata/converterSuite.TestNoVariants.txt b/gvcf2vcfbed/testdata/converterSuite.TestNoVariants.txt
index 3c398de5b94ef3a3d1156fe2bf0383228b2ac50b..f88ad141ac069cf474ed8fd092599ef35ccff963 100644 (file)
--- a/gvcf2vcfbed/testdata/converterSuite.TestNoVariants.txt
+++ b/gvcf2vcfbed/testdata/converterSuite.TestNoVariants.txt
@@ -5,7 +5,7 @@
 chr22  1       .       N       <NON_REF>       .       .       END=10510064    GT:DP:GQ:MIN_DP:PL      0/0:0:0:0:0,0,0
 chr22  10510065        .       A       <NON_REF>       .       .       END=10510079    GT:DP:GQ:MIN_DP:PL      0/0:1:3:1:0,3,35
 chr22  10510080        .       A       <NON_REF>       .       .       END=10510080    GT:DP:GQ:MIN_DP:PL      0/0:1:3:1:0,3,14
-chr22  10510081        .       G       <NON_REF>       .       .       END=10510147    GT:DP:GQ:MIN_DP:PL      0/0:1:3:1:0,3,35
+chr22  10510081        .       G       <NON_REF>       .       .       END=10510395    GT:DP:GQ:MIN_DP:PL      0/0:1:3:1:0,3,35
 chr22  10510396        .       T       <NON_REF>       .       .       END=10510396    GT:DP:GQ:MIN_DP:PL      0/0:8:24:8:0,24,278
 chr22  10510397        .       C       <NON_REF>       .       .       END=10510397    GT:DP:GQ:MIN_DP:PL      0/0:8:24:8:0,24,258
 chr22  10510398        .       T       <NON_REF>       .       .       END=10510398    GT:DP:GQ:MIN_DP:PL      0/0:8:24:8:0,24,278
@@ -81,10 +81,7 @@ chr22        10510650        .       T       <NON_REF>       .       .       END=50818468    GT:DP:GQ:MIN_DP:PL      0/0:0:0:0:0,0,0
 
 ===
 
-chr22  0       10510186
-chr22  10510202        10510234
-chr22  10510309        10510384
-chr22  10510388        10510389
+chr22  0       10510395
 chr22  10510426        10510427
 chr22  10510454        10510456
 chr22  10510579        10510583