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[Update] regresion tests: primerstrim and unified diff
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- slightly different read-counts with new primerstrim cutoff
- use unified diff for context and simpler patching
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@DrYak
DrYak committed Dec 29, 2024
1 parent 2afbf4c commit 353078b
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Showing 2 changed files with 14 additions and 14 deletions.
26 changes: 13 additions & 13 deletions ...puts/regression_tests_sars-cov-2/results/pos_MN908947_3_1/20200729/variants/SNVs/snvs.vcf
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion tests/regression_tests.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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