debian/patches/series

-Fix_Makefile.patch
-Disable_opt.patch

debian/tests/control

+Tests: run-sample-analysis
+Depends: @

debian/tests/output_tests/README

+# 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

+ 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

+ CHR  SNP   A1   A2          MAF  NCHROBS
+   1  rs0    0    1            0        2
+   1 rs10    2    1         0.25        4

debian/tests/run-sample-analysis

+#!/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/*
+