From 58adf3efe8ddde92f0158c1bb8c835e5c3be5716 Mon Sep 17 00:00:00 2001 From: Harrison Deng Date: Tue, 27 Jun 2023 14:03:33 +0000 Subject: [PATCH] Added required test resource --- .../expected_out/test_files_shortened.vcf | 17 ----------------- .../resources/test_files_shortened_haploid.vcf | 17 +++++++++++++++++ 2 files changed, 17 insertions(+), 17 deletions(-) delete mode 100644 tests/resources/expected_out/test_files_shortened.vcf create mode 100644 tests/resources/test_files_shortened_haploid.vcf diff --git a/tests/resources/expected_out/test_files_shortened.vcf b/tests/resources/expected_out/test_files_shortened.vcf deleted file mode 100644 index b867dc6..0000000 --- a/tests/resources/expected_out/test_files_shortened.vcf +++ /dev/null @@ -1,17 +0,0 @@ -##fileformat=VCFv4.1 -##fileDate=10122015_22h01m13s -##source=SHAPEIT2.v837 -##log_file=shapeit_10122015_22h01m13s_3f764d75-2fbb-42df-ab75-8c2dfd5731ce.log -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Gambian Chinese French Brazilian Nigerian Pakistani English Colombian Indian Japanese -1 846808 rs4475691 C T 100 . AC=1276;AN=5008;DP=20368 GT 1|1 0|0 0|0 ./. 0|0 0|0 0|0 0|0 ./. 0|0 -1 846854 rs111957712 G A 100 . AC=114;AN=5008;DP=20538 GT ./. 0|0 0|0 0|0 0|0 0|0 ./. ./. 0|0 0|0 -1 846864 rs950122 G C 100 . AC=1116;AN=5008;DP=20582 GT 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 ./. 0|0 -1 847228 rs3905286 C T 100 . AC=1215;AN=5008;DP=20731 GT 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 -1 847297 rs11507768 G A 100 . AC=359;AN=5008;DP=20809 GT 1|0 0|0 0|0 ./. 0|0 0|0 ./. 0|0 0|0 0|0 -1 847491 rs28407778 G A 100 . AC=1262;AN=5008;DP=16939 GT 1|1 0|0 0|0 0|0 0|0 ./. 0|0 0|0 0|1 0|0 -1 848023 rs144407116 C A 100 . AC=52;AN=5008;DP=22562 GT 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 -1 848090 rs4246505 G A 100 . AC=857;AN=5008;DP=19301 GT 0|0 0|0 0|0 0|0 0|0 0|0 ./. 0|0 ./. 0|0 -1 848445 rs4626817 G A 100 . AC=1255;AN=5008;DP=18444 GT 1|1 0|0 0|0 0|0 0|0 0|0 0|0 ./. ./. 0|0 -1 848456 rs11507767 A G 100 . AC=1266;AN=5008;DP=18137 GT 1|1 ./. 0|0 0|0 0|0 0|0 0|0 0|0 0|1 ./. -1 848738 rs3829741 C T 100 . AC=855;AN=5008;DP=16663 GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 diff --git a/tests/resources/test_files_shortened_haploid.vcf b/tests/resources/test_files_shortened_haploid.vcf new file mode 100644 index 0000000..4c526fd --- /dev/null +++ b/tests/resources/test_files_shortened_haploid.vcf @@ -0,0 +1,17 @@ +##fileformat=VCFv4.1 +##fileDate=10122015_22h01m13s +##source=SHAPEIT2.v837 +##log_file=shapeit_10122015_22h01m13s_3f764d75-2fbb-42df-ab75-8c2dfd5731ce.log +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Gambian Chinese French Brazilian Nigerian Pakistani English Colombian Indian Japanese +1 846808 rs4475691 C T 100 . AC=1276;AN=5008;DP=20368 GT:GQ:DP 1:70:60 0:30:10 0:20:40 ./.:0:0 0:70:60 0:90:30 0:80:70 0:50:80 ./.:0:0 0:100:80 +1 846854 rs111957712 G A 100 . AC=114;AN=5008;DP=20538 GT:GQ:DP ./.:0:0 0:40:30 0:80:30 0:0:20 0:40:80 0:10:30 ./.:0:0 ./.:0:0 0:70:0 0:90:30 +1 846864 rs950122 G C 100 . AC=1116;AN=5008;DP=20582 GT:GQ:DP 1:60:0 0:20:0 0:90:70 0:80:50 0:80:30 0:10:80 0:100:20 0:30:40 ./.:0:0 0:30:90 +1 847228 rs3905286 C T 100 . AC=1215;AN=5008;DP=20731 GT:GQ:DP 1:70:80 0:90:80 0:60:50 0:60:90 0:30:40 0:70:10 0:100:80 0:100:50 0:70:100 0:40:40 +1 847297 rs11507768 G A 100 . AC=359;AN=5008;DP=20809 GT:GQ:DP 1:0:60 0:10:30 0:80:60 ./.:0:0 0:10:100 0:10:100 ./.:0:0 0:100:40 0:20:20 0:10:0 +1 847491 rs28407778 G A 100 . AC=1262;AN=5008;DP=16939 GT:GQ:DP 1:0:100 0:70:40 0:0:60 0:90:90 0:90:90 ./.:0:0 0:70:60 0:70:0 0:90:100 0:60:60 +1 848023 rs144407116 C A 100 . AC=52;AN=5008;DP=22562 GT:GQ:DP 0:10:60 0:20:80 0:20:50 0:20:90 0:90:10 0:70:60 0:40:30 0:60:0 0:40:40 0:10:10 +1 848090 rs4246505 G A 100 . AC=857;AN=5008;DP=19301 GT:GQ:DP 0:70:70 0:90:30 0:40:10 0:80:20 0:50:50 0:10:30 ./.:0:0 0:20:60 ./.:0:0 0:90:0 +1 848445 rs4626817 G A 100 . AC=1255;AN=5008;DP=18444 GT:GQ:DP 1:100:40 0:80:90 0:30:100 0:100:60 0:40:90 0:20:30 0:70:100 ./.:0:0 ./.:0:0 0:80:30 +1 848456 rs11507767 A G 100 . AC=1266;AN=5008;DP=18137 GT:GQ:DP 1:40:30 ./.:0:0 0:60:90 0:60:40 0:100:80 0:50:50 0:0:10 0:60:0 0:100:100 ./.:0:0 +1 848738 rs3829741 C T 100 . AC=855;AN=5008;DP=16663 GT:GQ:DP 0:50:90 0:50:50 0:50:30 0:60:60 0:80:40 0:50:80 0:0:80 0:0:30 0:10:0 0:70:30