diff -Nru andi-0.12/debian/changelog andi-0.12/debian/changelog
--- andi-0.12/debian/changelog	2017-08-09 08:25:35.000000000 +0000
+++ andi-0.12/debian/changelog	2018-03-07 11:12:24.000000000 +0000
@@ -1,3 +1,20 @@
+andi (0.12-3) unstable; urgency=medium
+
+  * Allow for parallelisation of unit tests. Really fixes build failures.
+
+ -- Fabian Klötzl <kloetzl@evolbio.mpg.de>  Wed, 07 Mar 2018 12:12:24 +0100
+
+andi (0.12-2) unstable; urgency=medium
+
+  [ Fabian Klötzl ]
+  * Derandomize unit tests. Fixes build failures.
+
+  [ Andreas Tille ]
+  * Standards-Version: 4.1.3
+  * debhelper 11
+
+ -- Fabian Klötzl <kloetzl@evolbio.mpg.de>  Mon, 05 Mar 2018 15:11:27 +0100
+
 andi (0.12-1) unstable; urgency=medium
 
   * Team upload.
diff -Nru andi-0.12/debian/compat andi-0.12/debian/compat
--- andi-0.12/debian/compat	2017-08-09 08:25:35.000000000 +0000
+++ andi-0.12/debian/compat	2018-03-07 11:12:24.000000000 +0000
@@ -1 +1 @@
-10
+11
diff -Nru andi-0.12/debian/control andi-0.12/debian/control
--- andi-0.12/debian/control	2017-08-09 08:25:35.000000000 +0000
+++ andi-0.12/debian/control	2018-03-07 11:12:24.000000000 +0000
@@ -3,12 +3,12 @@
 Uploaders: Fabian Klötzl <kloetzl@evolbio.mpg.de>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                libdivsufsort-dev,
                pkgconf,
                libgsl-dev,
                libglib2.0-dev
-Standards-Version: 4.0.0
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/andi.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/andi.git
 Homepage: https://github.com/EvolBioInf/andi
diff -Nru andi-0.12/debian/patches/0001-Make-unit-tests-reproducible.patch andi-0.12/debian/patches/0001-Make-unit-tests-reproducible.patch
--- andi-0.12/debian/patches/0001-Make-unit-tests-reproducible.patch	1970-01-01 00:00:00.000000000 +0000
+++ andi-0.12/debian/patches/0001-Make-unit-tests-reproducible.patch	2018-03-07 11:12:24.000000000 +0000
@@ -0,0 +1,162 @@
+From: Fabian Klötzl <kloetzl@evolbio.mpg.de>
+Date: Mon, 5 Mar 2018 14:43:06 +0100
+Subject: Make unit tests reproducible
+Applied-Upstream: https://github.com/EvolBioInf/andi/commit/394c3b4c3dfb8fd40530fd6815f300a273a309d2
+
+---
+ test/low_homo.sh   | 15 ++++++++++++---
+ test/nan.sh        | 12 ++++++++++--
+ test/test_extra.sh | 15 ++++++++++++---
+ test/test_join.sh  | 40 ++++++++++++++++++++++++++++++++--------
+ 4 files changed, 66 insertions(+), 16 deletions(-)
+
+diff --git a/test/low_homo.sh b/test/low_homo.sh
+index 72d1693..11e889e 100755
+--- a/test/low_homo.sh
++++ b/test/low_homo.sh
+@@ -1,8 +1,17 @@
+ #!/bin/bash -f
+ 
+-./test/test_fasta -l 100000 > a.fa
+-./test/test_fasta -l 100000 > b.fa
+-./test/test_fasta -l 100 > both.fa
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++SEED3=0
++if test $SEED -ne 0; then
++	SEED=$((SEED + 1))
++	SEED2=$((SEED + 2))
++	SEED3=$((SEED + 3))
++fi
++
++./test/test_fasta -s $SEED -l 100000 > a.fa
++./test/test_fasta -s $SEED2 -l 100000 > b.fa
++./test/test_fasta -s $SEED3 -l 100 > both.fa
+ 
+ cat both.fa a.fa | awk -vRS='>' '{if($1 == "S0")print ">"$0 > "S0.fa"}'
+ cat both.fa b.fa | awk -vRS='>' '{if($1 == "S1")print ">"$0 > "S1.fa"}'
+diff --git a/test/nan.sh b/test/nan.sh
+index e0502d0..60db0e2 100755
+--- a/test/nan.sh
++++ b/test/nan.sh
+@@ -1,7 +1,15 @@
+ #!/bin/bash -f
+ 
+-./test/test_fasta -l 10000 > a.fa
+-./test/test_fasta -l 10000 > b.fa
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++if test $SEED -ne 0; then
++	SEED=$((SEED + 1))
++	SEED2=$((SEED + 2))
++fi
++
++
++./test/test_fasta -s $SEED -l 10000 > a.fa
++./test/test_fasta -s $SEED2 -l 10000 > b.fa
+ 
+ # this is expected to trigger the nan warning
+ ./src/andi -j a.fa b.fa 2>&1 | grep 'nan'
+diff --git a/test/test_extra.sh b/test/test_extra.sh
+index dbb23ea..c1c0641 100755
+--- a/test/test_extra.sh
++++ b/test/test_extra.sh
+@@ -3,17 +3,26 @@
+ # Test if andi exists, and can be executed
+ ./src/andi --version > /dev/null || exit 1
+ 
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++SEED3=0
++if test $SEED -ne 0; then
++        SEED=$((SEED + 1))
++        SEED2=$((SEED + 2))
++        SEED3=$((SEED + 3))
++fi
++
+ # Test andi for more than just two sequences at a time
+-./test/test_fasta -l 100000 -d 0.01 -d 0.01 -d 0.01 -d 0.01 | ./src/andi > /dev/null || exit 1
++./test/test_fasta -s $SEED -l 100000 -d 0.01 -d 0.01 -d 0.01 -d 0.01 | ./src/andi > /dev/null || exit 1
+ 
+ # Test low-memory mode
+-./test/test_fasta -l 10000 > test_extra.fasta
++./test/test_fasta -s $SEED2 -l 10000 > test_extra.fasta
+ ./src/andi test_extra.fasta > extra.out
+ ./src/andi test_extra.fasta --low-memory > extra_low_memory.out
+ diff extra.out extra_low_memory.out || exit 1
+ 
+ # Test file of filenames
+-./test/test_fasta -l 10000 > test_extra.fasta
++./test/test_fasta -s $SEED3 -l 10000 > test_extra.fasta
+ echo "$PWD/test_extra.fasta" > fof.txt
+ ./src/andi test_extra.fasta > extra.out
+ ./src/andi --file-of-filenames fof.txt > fof.out
+diff --git a/test/test_join.sh b/test/test_join.sh
+index 60e099a..33cc2c6 100755
+--- a/test/test_join.sh
++++ b/test/test_join.sh
+@@ -2,10 +2,19 @@
+ 
+ ./src/andi --help > /dev/null || exit 1
+ 
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++SEED3=0
++if test $SEED -ne 0; then
++        SEED=$((SEED + 1))
++        SEED2=$((SEED + 2))
++        SEED3=$((SEED + 3))
++fi
++
+ # Simple join test
+-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p1.fasta
+-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p2.fasta
+-./test/test_fasta -l 10000 -L 10000 -d 0.1 > p3.fasta
++./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1.fasta
++./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2.fasta
++./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3.fasta
+ 
+ head -qn 2 p1.fasta p2.fasta p3.fasta > S0.fasta
+ tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta
+@@ -25,9 +34,16 @@ if test $RES -ne 1; then
+ 	exit 1;
+ fi
+ 
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++if test $SEED -ne 0; then
++        SEED=$((SEED + 5))
++        SEED2=$((SEED + 6))
++fi
++
+ #unbalanced number of contigs
+-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p2.fasta
+-./test/test_fasta -l 10000 -L 10000 -d 0.1 > p3.fasta
++./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p2.fasta
++./test/test_fasta -s $SEED2 -l 10000 -L 10000 -d 0.1 > p3.fasta
+ 
+ head -qn 2 p3.fasta > S0.fasta
+ tail -qn 2 p2.fasta p3.fasta > S1.fasta
+@@ -47,11 +63,19 @@ if test $RES -ne 1; then
+         exit 1;
+ fi
+ 
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++SEED3=0
++if test $SEED -ne 0; then
++        SEED=$((SEED + 11))
++        SEED2=$((SEED + 12))
++        SEED3=$((SEED + 13))
++fi
+ 
+ #unbalanced number of contigs 2
+-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p1.fasta
+-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p2.fasta
+-./test/test_fasta -l 10000 -L 10000 -d 0.1 > p3.fasta
++./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1.fasta
++./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2.fasta
++./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3.fasta
+ 
+ head -qn 2 p1.fasta p3.fasta > S0.fasta
+ tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta
diff -Nru andi-0.12/debian/patches/0002-prefix-files-in-unit-tests.patch andi-0.12/debian/patches/0002-prefix-files-in-unit-tests.patch
--- andi-0.12/debian/patches/0002-prefix-files-in-unit-tests.patch	1970-01-01 00:00:00.000000000 +0000
+++ andi-0.12/debian/patches/0002-prefix-files-in-unit-tests.patch	2018-03-07 11:12:24.000000000 +0000
@@ -0,0 +1,182 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian@kloetzl.info>
+Date: Wed, 7 Mar 2018 11:26:26 +0100
+Subject: prefix files in unit tests
+Applied-Upstream: https://github.com/EvolBioInf/andi/commit/e35d1a51f71541f246919a277386817f69c94a3e
+
+Unit tests can be run in parallel (see debian builds). Thus they should
+work on different files, otherwise bad and confusing things happen.
+---
+ test/low_homo.sh  | 16 ++++++++--------
+ test/nan.sh       | 10 +++++-----
+ test/test_join.sh | 48 ++++++++++++++++++++++++------------------------
+ 3 files changed, 37 insertions(+), 37 deletions(-)
+
+diff --git a/test/low_homo.sh b/test/low_homo.sh
+index 11e889e..1f16a79 100755
+--- a/test/low_homo.sh
++++ b/test/low_homo.sh
+@@ -9,21 +9,21 @@ if test $SEED -ne 0; then
+ 	SEED3=$((SEED + 3))
+ fi
+ 
+-./test/test_fasta -s $SEED -l 100000 > a.fa
+-./test/test_fasta -s $SEED2 -l 100000 > b.fa
+-./test/test_fasta -s $SEED3 -l 100 > both.fa
++./test/test_fasta -s $SEED -l 100000 > a_low.fa
++./test/test_fasta -s $SEED2 -l 100000 > b_low.fa
++./test/test_fasta -s $SEED3 -l 100 > both_low.fa
+ 
+-cat both.fa a.fa | awk -vRS='>' '{if($1 == "S0")print ">"$0 > "S0.fa"}'
+-cat both.fa b.fa | awk -vRS='>' '{if($1 == "S1")print ">"$0 > "S1.fa"}'
++cat both_low.fa a_low.fa | awk -vRS='>' '{if($1 == "S0")print ">"$0 > "S0_low.fa"}'
++cat both_low.fa b_low.fa | awk -vRS='>' '{if($1 == "S1")print ">"$0 > "S1_low.fa"}'
+ 
+ # this is expected to trigger the low homology warning
+-./src/andi -j S0.fa S1.fa 2>&1 | grep 'homology'
++./src/andi -j S0_low.fa S1_low.fa 2>&1 | grep 'homology'
+ EXIT_VAL=$?
+ 
+ if [[ EXIT_VAL -ge 1 ]]; then
+ 	echo "Triggering low homology failed" >&2
+-	grep '^>' a.fa b.fa both.fa
++	grep '^>' a_low.fa b_low.fa both_low.fa
+ fi
+ 
+-rm -f a.fa b.fa both.fa S0.fa S1.fa
++rm -f a_low.fa b_low.fa both_low.fa S0_low.fa S1_low.fa
+ exit $EXIT_VAL
+diff --git a/test/nan.sh b/test/nan.sh
+index 60db0e2..97fa167 100755
+--- a/test/nan.sh
++++ b/test/nan.sh
+@@ -8,18 +8,18 @@ if test $SEED -ne 0; then
+ fi
+ 
+ 
+-./test/test_fasta -s $SEED -l 10000 > a.fa
+-./test/test_fasta -s $SEED2 -l 10000 > b.fa
++./test/test_fasta -s $SEED -l 10000 > a_nan.fa
++./test/test_fasta -s $SEED2 -l 10000 > b_nan.fa
+ 
+ # this is expected to trigger the nan warning
+-./src/andi -j a.fa b.fa 2>&1 | grep 'nan'
++./src/andi -j a_nan.fa b_nan.fa 2>&1 | grep 'nan'
+ EXIT_VAL=$?
+ 
+ 
+ if [[ EXIT_VAL -ge 1 ]]; then
+ 	echo "Triggering nan failed" >&2
+-	grep '^>' a.fa b.fa both.fa
++	grep '^>' a_nan.fa b_nan.fa
+ fi
+ 
+-rm -f a.fa b.fa
++rm -f a_nan.fa b_nan.fa
+ exit $EXIT_VAL
+diff --git a/test/test_join.sh b/test/test_join.sh
+index 33cc2c6..a0616bf 100755
+--- a/test/test_join.sh
++++ b/test/test_join.sh
+@@ -12,17 +12,17 @@ if test $SEED -ne 0; then
+ fi
+ 
+ # Simple join test
+-./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1.fasta
+-./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2.fasta
+-./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3.fasta
++./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1_join.fasta
++./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2_join.fasta
++./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3_join.fasta
+ 
+-head -qn 2 p1.fasta p2.fasta p3.fasta > S0.fasta
+-tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta
++head -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S0_join.fasta
++tail -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S1_join.fasta
+ 
+-rm p1.fasta p2.fasta p3.fasta;
++rm p1_join.fasta p2_join.fasta p3_join.fasta;
+ 
+ 
+-RES=$(./src/andi -m RAW -t 1 -j S0.fasta S1.fasta |
++RES=$(./src/andi -m RAW -t 1 -j S0_join.fasta S1_join.fasta |
+ 	tail -n 1 |
+ 	awk '{print ($2 - 0.1)}' |
+ 	awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}'
+@@ -30,7 +30,7 @@ RES=$(./src/andi -m RAW -t 1 -j S0.fasta S1.fasta |
+ 
+ if test $RES -ne 1; then
+ 	echo "The last test computed a distance deviating more than three percent from its intended value."
+-	echo "See S0.fasta and S1.fasta for the used sequences."
++	echo "See S0_join.fasta and S1_join.fasta for the used sequences."
+ 	exit 1;
+ fi
+ 
+@@ -42,16 +42,16 @@ if test $SEED -ne 0; then
+ fi
+ 
+ #unbalanced number of contigs
+-./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p2.fasta
+-./test/test_fasta -s $SEED2 -l 10000 -L 10000 -d 0.1 > p3.fasta
++./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p2_join.fasta
++./test/test_fasta -s $SEED2 -l 10000 -L 10000 -d 0.1 > p3_join.fasta
+ 
+-head -qn 2 p3.fasta > S0.fasta
+-tail -qn 2 p2.fasta p3.fasta > S1.fasta
++head -qn 2 p3_join.fasta > S0_join.fasta
++tail -qn 2 p2_join.fasta p3_join.fasta > S1_join.fasta
+ 
+-rm p2.fasta p3.fasta;
++rm p2_join.fasta p3_join.fasta;
+ 
+ 
+-RES=$(./src/andi -m RAW -t1 -j S0.fasta S1.fasta |
++RES=$(./src/andi -m RAW -t1 -j S0_join.fasta S1_join.fasta |
+         tail -n 1 |
+         awk '{print ($2 - 0.1)}' |
+         awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}'
+@@ -59,7 +59,7 @@ RES=$(./src/andi -m RAW -t1 -j S0.fasta S1.fasta |
+ 
+ if test $RES -ne 1; then
+         echo "The last test computed a distance deviating more than three percent from its intended value."
+-        echo "See S0.fasta and S1.fasta for the used sequences."
++        echo "See S0_join.fasta and S1_join.fasta for the used sequences."
+         exit 1;
+ fi
+ 
+@@ -73,17 +73,17 @@ if test $SEED -ne 0; then
+ fi
+ 
+ #unbalanced number of contigs 2
+-./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1.fasta
+-./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2.fasta
+-./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3.fasta
++./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1_join.fasta
++./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2_join.fasta
++./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3_join.fasta
+ 
+-head -qn 2 p1.fasta p3.fasta > S0.fasta
+-tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta
++head -qn 2 p1_join.fasta p3_join.fasta > S0_join.fasta
++tail -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S1_join.fasta
+ 
+-rm p1.fasta p2.fasta p3.fasta;
++rm p1_join.fasta p2_join.fasta p3_join.fasta;
+ 
+ 
+-RES=$(./src/andi -mRAW -t 1 -j S0.fasta S1.fasta |
++RES=$(./src/andi -mRAW -t 1 -j S0_join.fasta S1_join.fasta |
+         tail -n 1 |
+         awk '{print ($2 - 0.1)}' |
+         awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}'
+@@ -91,9 +91,9 @@ RES=$(./src/andi -mRAW -t 1 -j S0.fasta S1.fasta |
+ 
+ if test $RES -ne 1; then
+         echo "The last test computed a distance deviating more than three percent from its intended value."
+-        echo "See S0.fasta and S1.fasta for the used sequences."
++        echo "See S0_join.fasta and S1_join.fasta for the used sequences."
+         exit 1;
+ fi
+ 
+ 
+-rm S0.fasta S1.fasta
++rm S0_join.fasta S1_join.fasta
diff -Nru andi-0.12/debian/patches/series andi-0.12/debian/patches/series
--- andi-0.12/debian/patches/series	1970-01-01 00:00:00.000000000 +0000
+++ andi-0.12/debian/patches/series	2018-03-07 11:12:24.000000000 +0000
@@ -0,0 +1,2 @@
+0001-Make-unit-tests-reproducible.patch
+0002-prefix-files-in-unit-tests.patch