From 353078b04822c93f94ad276a73ccc7816a05aee9 Mon Sep 17 00:00:00 2001 From: Ivan Blagoev Topolsky Date: Sun, 29 Dec 2024 13:41:01 +0100 Subject: [PATCH] [Update] regresion tests: primerstrim and unified diff - slightly different read-counts with new primerstrim cutoff - use unified diff for context and simpler patching --- .../20200729/variants/SNVs/snvs.vcf | 26 +++++++++---------- tests/regression_tests.sh | 2 +- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/tests/expected_outputs/regression_tests_sars-cov-2/results/pos_MN908947_3_1/20200729/variants/SNVs/snvs.vcf b/tests/expected_outputs/regression_tests_sars-cov-2/results/pos_MN908947_3_1/20200729/variants/SNVs/snvs.vcf index cf6a9c61..afc677c9 100644 --- a/tests/expected_outputs/regression_tests_sars-cov-2/results/pos_MN908947_3_1/20200729/variants/SNVs/snvs.vcf +++ b/tests/expected_outputs/regression_tests_sars-cov-2/results/pos_MN908947_3_1/20200729/variants/SNVs/snvs.vcf @@ -21,19 +21,19 @@ ##bcftools_concatVersion=1.10.2+htslib-1.10.2 ##bcftools_concatCommand=concat -o /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/snvs_tmp.vcf /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_1/snv/SNVs_0.010000_final.vcf.gz /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_2/snv/SNVs_0.010000_final.vcf.gz /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_3/snv/SNVs_0.010000_final.vcf.gz /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_4/snv/SNVs_0.010000_final.vcf.gz /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_5/snv/SNVs_0.010000_final.vcf.gz /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_6/snv/SNVs_0.010000_final.vcf.gz /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_7/snv/SNVs_0.010000_final.vcf.gz /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_8/snv/SNVs_0.010000_final.vcf.gz /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_9/snv/SNVs_0.010000_final.vcf.gz /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_10/snv/SNVs_0.010000_final.vcf.gz /tmp/tmp.qHFx7sYjwN/results/pos_MN908947_3_1/20200729/variants/SNVs/REGION_11/snv/SNVs_0.010000_final.vcf.gz; Date=Tue Aug 16 01:59:44 2022 #CHROM POS ID REF ALT QUAL FILTER INFO -NC_045512.2 13451 . G - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=11;Rvar=11;Ftot=240;Rtot=214;Pval=0.955858;Qval=1 -NC_045512.2 13452 . C - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=11;Rvar=11;Ftot=240;Rtot=214;Pval=0.955858;Qval=1 -NC_045512.2 13453 . A - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=11;Rvar=11;Ftot=240;Rtot=215;Pval=0.963863;Qval=1 -NC_045512.2 13454 . C - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=240;Rtot=215;Pval=0.92476;Qval=1 -NC_045512.2 13455 . A - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=240;Rtot=217;Pval=0.942194;Qval=1 -NC_045512.2 13456 . A - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=240;Rtot=217;Pval=0.942194;Qval=1 -NC_045512.2 13457 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=240;Rtot=219;Pval=0.959498;Qval=1 -NC_045512.2 13458 . C - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=240;Rtot=219;Pval=0.959498;Qval=1 -NC_045512.2 13459 . G - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=240;Rtot=220;Pval=0.968099;Qval=1 -NC_045512.2 13460 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=240;Rtot=220;Pval=0.968099;Qval=1 -NC_045512.2 13461 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=240;Rtot=221;Pval=0.976666;Qval=1 -NC_045512.2 13462 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=240;Rtot=221;Pval=0.976666;Qval=1 -NC_045512.2 13463 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=240;Rtot=221;Pval=0.976666;Qval=1 +NC_045512.2 13451 . G - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=11;Rvar=11;Ftot=239;Rtot=214;Pval=0.963028;Qval=1 +NC_045512.2 13452 . C - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=11;Rvar=11;Ftot=239;Rtot=214;Pval=0.963028;Qval=1 +NC_045512.2 13453 . A - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=11;Rvar=11;Ftot=239;Rtot=215;Pval=0.971037;Qval=1 +NC_045512.2 13454 . C - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=215;Pval=0.932617;Qval=1 +NC_045512.2 13455 . A - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=217;Pval=0.950066;Qval=1 +NC_045512.2 13456 . A - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=217;Pval=0.950066;Qval=1 +NC_045512.2 13457 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=219;Pval=0.967381;Qval=1 +NC_045512.2 13458 . C - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=219;Pval=0.967381;Qval=1 +NC_045512.2 13459 . G - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=220;Pval=0.975986;Qval=1 +NC_045512.2 13460 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=220;Pval=0.975986;Qval=1 +NC_045512.2 13461 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=221;Pval=0.984556;Qval=1 +NC_045512.2 13462 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=221;Pval=0.984556;Qval=1 +NC_045512.2 13463 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=221;Pval=0.984556;Qval=1 NC_045512.2 13464 . T - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=221;Pval=0.984556;Qval=1 NC_045512.2 13465 . A - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=221;Pval=0.984556;Qval=1 NC_045512.2 13466 . A - 4.77121 PASS Freq1=0;Freq2=0.1246;Freq3=0.0826;Post1=0;Post2=1;Post3=1;Fvar=14;Rvar=14;Ftot=239;Rtot=222;Pval=0.99309;Qval=1 diff --git a/tests/regression_tests.sh b/tests/regression_tests.sh index 35d2a040..3275dfb1 100755 --- a/tests/regression_tests.sh +++ b/tests/regression_tests.sh @@ -156,7 +156,7 @@ function compare_to_recorded_results { while IFS= read -r -d '' RECORDED_OUTPUT; do CURRENT_OUTPUT=${PROJECT_DIR}/${RECORDED_OUTPUT} echo "COMPARE ${RECORDED_OUTPUT} AND ${CURRENT_OUTPUT}" - if diff -I '^#' "${RECORDED_OUTPUT}" "${CURRENT_OUTPUT}" >> "${DIFF_FILE}"; then + if diff -u -a -I '^#' "${RECORDED_OUTPUT}" "${CURRENT_OUTPUT}" >> "${DIFF_FILE}"; then : else echo