[med-svn] [Git][med-team/plink2][master] 2 commits: Disable all patches

[Dylan Aïssi]

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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20191120/51edce3d/attachment-0001.html>