Dylan Aïssi pushed to branch master at Debian Med / plink2
Commits: c972f9bc by Dylan Aïssi at 2019-11-20T06:03:27Z Disable all patches - - - - - 7c671e79 by Dylan Aïssi at 2019-11-20T06:26:40Z Add draft tests - - - - - 6 changed files: - debian/patches/series - + debian/tests/control - + debian/tests/output_tests/README - + debian/tests/output_tests/expected.plink.assoc - + debian/tests/output_tests/expected.plink.frq - + debian/tests/run-sample-analysis Changes: ===================================== debian/patches/series ===================================== @@ -1,2 +0,0 @@ -Fix_Makefile.patch -Disable_opt.patch ===================================== debian/tests/control ===================================== @@ -0,0 +1,2 @@ +Tests: run-sample-analysis +Depends: @ ===================================== debian/tests/output_tests/README ===================================== @@ -0,0 +1,10 @@ +# Output files (i.e. expected.plink.assoc and expected.plink.frq) were generated following: + +wget https://www.cog-genomics.org/static/bin/plink141220/plink_linux_x86_64.zip +unzip plink_linux_x86_64.zip + +./plink --file toy --freq +mv plink.frq expected.plink.frq + +./plink --file toy --assoc +mv plink.assoc expected.plink.assoc ===================================== debian/tests/output_tests/expected.plink.assoc ===================================== @@ -0,0 +1,3 @@ + CHR SNP BP A1 F_A F_U A2 CHISQ P OR + 1 rs0 1000 0 0 NA 1 NA NA NA + 1 rs10 1001 2 0.5 0 1 1.333 0.2482 NA ===================================== debian/tests/output_tests/expected.plink.frq ===================================== @@ -0,0 +1,3 @@ + CHR SNP A1 A2 MAF NCHROBS + 1 rs0 0 1 0 2 + 1 rs10 2 1 0.25 4 ===================================== debian/tests/run-sample-analysis ===================================== @@ -0,0 +1,22 @@ +#!/bin/sh -e +# http://dep.debian.net/deps/dep8/ + +pkg=plink2 +if [ "$AUTOPKGTEST_TMP" = "" ] ; then + AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` +fi +cd $AUTOPKGTEST_TMP +cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP + +PLINK2_TEST='plink2 --file toy' + +# Allele frequencies +$PLINK2_TEST --freq +diff plink.frq expected.plink.frq + +# Case/control or QTL association +$PLINK2_TEST --assoc +diff plink.assoc expected.plink.assoc + +rm -f $AUTOPKGTEST_TMP/* + View it on GitLab: https://salsa.debian.org/med-team/plink2/compare/02bf6ac56c24dbf785673c92671d6659c313d32f...7c671e799caee5625b584ed75fc3fb5ae422c1f6 -- View it on GitLab: https://salsa.debian.org/med-team/plink2/compare/02bf6ac56c24dbf785673c92671d6659c313d32f...7c671e799caee5625b584ed75fc3fb5ae422c1f6 You're receiving this email because of your account on salsa.debian.org.
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