diff -pruN 1.4.1-2/debian/changelog 1.4.1-3/debian/changelog
--- 1.4.1-2/debian/changelog	2022-07-23 19:23:15.000000000 +0000
+++ 1.4.1-3/debian/changelog	2022-08-03 11:15:25.000000000 +0000
@@ -1,3 +1,12 @@
+abpoa (1.4.1-3) unstable; urgency=medium
+
+  * d/t/run-unit-test: do not run if a simd specific file is missing.
+  * d/t/run-unit-test: compare deterministic results to reference data.
+  * d/rules: move preprocessor flags definition to CPPFLAGS.
+  * d/rules: SIMDe: enable native aliases in CPPFLAGS. (Closes: #1016207)
+
+ -- Étienne Mollier <emollier@debian.org>  Wed, 03 Aug 2022 13:15:25 +0200
+
 abpoa (1.4.1-2) unstable; urgency=medium
 
   * Source-only upload.
diff -pruN 1.4.1-2/debian/rules 1.4.1-3/debian/rules
--- 1.4.1-2/debian/rules	2022-07-23 19:23:15.000000000 +0000
+++ 1.4.1-3/debian/rules	2022-08-03 11:15:25.000000000 +0000
@@ -3,9 +3,11 @@
 export LC_ALL=C.UTF-8
 
 include /usr/share/dpkg/default.mk
-export DEB_BUILD_MAINT_OPTIONS=hardening=+all
-export DEB_CFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
-export DEB_CXXFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_CPPFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP
+export DEB_CPPFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_NATIVE_ALIASES
+export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3
+export DEB_CXXFLAGS_MAINT_APPEND += -fopenmp-simd -O3
 export PYBUILD_NAME=pyabpoa
 
 %:
@@ -24,7 +26,6 @@ ifeq ($(DEB_HOST_ARCH),amd64)
 endif
 	dh_auto_build --buildsystem=makefile -- all
 	mv -v bin/abpoa bin/abpoa.generic
-	# copy the dispatch script
 	cp debian/abpoa-dispatch.sh bin/abpoa
 
 override_dh_auto_test:
diff -pruN 1.4.1-2/debian/tests/run-unit-test 1.4.1-3/debian/tests/run-unit-test
--- 1.4.1-2/debian/tests/run-unit-test	2022-07-23 19:23:15.000000000 +0000
+++ 1.4.1-3/debian/tests/run-unit-test	2022-08-03 11:15:25.000000000 +0000
@@ -17,27 +17,779 @@ cd "${AUTOPKGTEST_TMP}"
 
 set -x
 
-# Test as many variants of the program as the test node permits
+# Test as many variants of the program as the test node permits.
 for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch
 do
 	if [ "$SIMDE" = "dispatch" ]
 	then BINARY="abpoa"
-	elif grep -q "$SIMDE" /proc/cpuinfo || [ "$SIMDE" = "generic" ]
+	elif { grep -q "$SIMDE" /proc/cpuinfo && [ -x "abpoa.$SIMDE" ] ; } \
+		|| [ "$SIMDE" = "generic" ]
 	then BINARY="abpoa.$SIMDE"
 	else continue
 	fi
 
-	# Tests inspired by the README.md document
+	# NOTES FOR TESTERS: tests are inspired by the README.md document.
+	# Reference data are tested with diff commands on the basis of the
+	# output of an initial version of the program.  If newer versions are
+	# outputing different values consistently, then it is well possible
+	# that the reference data in the autopkgtest needs being updated.
+
 	"$BINARY" ./test_data/seq.fa > cons.fa
+	diff - cons.fa << END
+>Consensus_sequence
+CGTCAATCTATCGAAGCATACGCGGCAGAGCCGAAGACCTCGGCAATCAC
+END
+
+	# Consensus data do not seem deterministic, so no reference data are
+	# provided for this test.
 	"$BINARY" ./test_data/heter.fa > 2cons.fa
+
 	"$BINARY" -r1 ./test_data/seq.fa > out.msa
+	diff - out.msa << END
+>1
+---CGTCAAT-CTA-TC--G---AAGCA---TACG--CGGGC-AGAGCC--GAA---GACCTCGG-CAATCCA--
+>2
+CCACGTCAAT-CTA-TC--G---AAGCA---TACG--C-GGC---AGCC--GAACTCGACCTCGG-CAATCAC--
+>3
+---CGTCAAT-CTA-TC--G---AAGCA---TACG--C-GGC-AGAGCCCGGAA---GACCTCGG-CAATCAC--
+>4
+---CGTCAATGCTAGTC--G---AAGCA---GCTG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATCAC--
+>5
+---CGTCAAT-CTA-TC--G---AAGCATTCTACG--C-GGC-AGAGCC--------GACCTCGG-CAATCAC--
+>6
+---CGTCAAT-CTA-----G---AAGCA---TACG--C-GGCAAGAGCC--GAA---GACCTCGGCCAATCAC--
+>7
+---CGTCAAT-CTA-TC--GGTAAAGCA---TACGCTC-TGT---AGCC--GAA---GACCTCGG-CAATCAC--
+>8
+---CGTCAAT-CTA-TCTTC---AAGCA---TACG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATC----
+>9
+---CGTCAAT-GGA-TC--G----AG-----TACG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATCAC--
+>10
+---CGTCAAT-CTAATC--G---AAGCA---TACG--C-GGC-AGAGCC--G---TCTACCTCGG-CAATCACGT
+END
+
 	"$BINARY" -r2 ./test_data/seq.fa > out_cons.msa
+	diff - out_cons.msa << END
+>1
+---CGTCAAT-CTA-TC--G---AAGCA---TACG--CGGGC-AGAGCC--GAA---GACCTCGG-CAATCCA--
+>2
+CCACGTCAAT-CTA-TC--G---AAGCA---TACG--C-GGC---AGCC--GAACTCGACCTCGG-CAATCAC--
+>3
+---CGTCAAT-CTA-TC--G---AAGCA---TACG--C-GGC-AGAGCCCGGAA---GACCTCGG-CAATCAC--
+>4
+---CGTCAATGCTAGTC--G---AAGCA---GCTG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATCAC--
+>5
+---CGTCAAT-CTA-TC--G---AAGCATTCTACG--C-GGC-AGAGCC--------GACCTCGG-CAATCAC--
+>6
+---CGTCAAT-CTA-----G---AAGCA---TACG--C-GGCAAGAGCC--GAA---GACCTCGGCCAATCAC--
+>7
+---CGTCAAT-CTA-TC--GGTAAAGCA---TACGCTC-TGT---AGCC--GAA---GACCTCGG-CAATCAC--
+>8
+---CGTCAAT-CTA-TCTTC---AAGCA---TACG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATC----
+>9
+---CGTCAAT-GGA-TC--G----AG-----TACG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATCAC--
+>10
+---CGTCAAT-CTAATC--G---AAGCA---TACG--C-GGC-AGAGCC--G---TCTACCTCGG-CAATCACGT
+>Consensus_sequence
+---CGTCAAT-CTA-TC--G---AAGCA---TACG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATCAC--
+END
+
 	"$BINARY" -r3 ./test_data/seq.fa > out.gfa
+	diff - out.gfa << END
+H	VN:Z:1.0	NS:i:87	NL:i:109	NP:i:10
+S	52	C
+S	53	C
+L	52	+	53	+	0M
+S	54	A
+L	53	+	54	+	0M
+S	1	C
+L	54	+	1	+	0M
+S	2	G
+L	1	+	2	+	0M
+S	3	T
+L	2	+	3	+	0M
+S	4	C
+L	3	+	4	+	0M
+S	5	A
+L	4	+	5	+	0M
+S	6	A
+L	5	+	6	+	0M
+S	7	T
+L	6	+	7	+	0M
+S	62	G
+L	7	+	62	+	0M
+S	82	G
+L	7	+	82	+	0M
+S	8	C
+L	7	+	8	+	0M
+L	62	+	8	+	0M
+S	83	G
+L	82	+	83	+	0M
+S	9	T
+L	8	+	9	+	0M
+S	10	A
+L	9	+	10	+	0M
+L	83	+	10	+	0M
+S	63	G
+L	10	+	63	+	0M
+S	84	A
+L	10	+	84	+	0M
+S	11	T
+L	10	+	11	+	0M
+L	63	+	11	+	0M
+L	84	+	11	+	0M
+S	12	C
+L	11	+	12	+	0M
+S	13	G
+L	12	+	13	+	0M
+L	10	+	13	+	0M
+S	79	T
+L	12	+	79	+	0M
+S	72	G
+L	13	+	72	+	0M
+S	80	T
+L	79	+	80	+	0M
+S	73	T
+L	72	+	73	+	0M
+S	81	C
+L	80	+	81	+	0M
+S	74	A
+L	73	+	74	+	0M
+S	14	A
+L	13	+	14	+	0M
+L	74	+	14	+	0M
+L	81	+	14	+	0M
+S	15	A
+L	14	+	15	+	0M
+L	13	+	15	+	0M
+S	16	G
+L	15	+	16	+	0M
+S	17	C
+L	16	+	17	+	0M
+S	18	A
+L	17	+	18	+	0M
+S	64	G
+L	18	+	64	+	0M
+S	67	T
+L	18	+	67	+	0M
+S	65	C
+L	64	+	65	+	0M
+S	68	T
+L	67	+	68	+	0M
+S	66	T
+L	65	+	66	+	0M
+S	69	C
+L	68	+	69	+	0M
+S	19	T
+L	18	+	19	+	0M
+L	69	+	19	+	0M
+L	16	+	19	+	0M
+S	20	A
+L	19	+	20	+	0M
+S	21	C
+L	20	+	21	+	0M
+S	22	G
+L	21	+	22	+	0M
+L	66	+	22	+	0M
+S	75	C
+L	22	+	75	+	0M
+S	76	T
+L	75	+	76	+	0M
+S	23	C
+L	22	+	23	+	0M
+L	76	+	23	+	0M
+S	24	G
+L	23	+	24	+	0M
+S	77	T
+L	23	+	77	+	0M
+S	25	G
+L	24	+	25	+	0M
+L	23	+	25	+	0M
+S	26	G
+L	25	+	26	+	0M
+L	77	+	26	+	0M
+S	27	C
+L	26	+	27	+	0M
+S	78	T
+L	26	+	78	+	0M
+S	70	A
+L	27	+	70	+	0M
+S	28	A
+L	27	+	28	+	0M
+L	70	+	28	+	0M
+S	29	G
+L	28	+	29	+	0M
+S	30	A
+L	29	+	30	+	0M
+L	27	+	30	+	0M
+L	78	+	30	+	0M
+S	31	G
+L	30	+	31	+	0M
+S	32	C
+L	31	+	32	+	0M
+S	33	C
+L	32	+	33	+	0M
+S	60	C
+L	33	+	60	+	0M
+S	61	G
+L	60	+	61	+	0M
+S	34	G
+L	33	+	34	+	0M
+L	61	+	34	+	0M
+S	35	A
+L	34	+	35	+	0M
+S	36	A
+L	35	+	36	+	0M
+S	55	C
+L	36	+	55	+	0M
+S	56	T
+L	55	+	56	+	0M
+L	34	+	56	+	0M
+S	57	C
+L	56	+	57	+	0M
+S	37	G
+L	36	+	37	+	0M
+L	57	+	37	+	0M
+L	33	+	37	+	0M
+S	85	T
+L	57	+	85	+	0M
+S	38	A
+L	37	+	38	+	0M
+L	85	+	38	+	0M
+S	39	C
+L	38	+	39	+	0M
+S	40	C
+L	39	+	40	+	0M
+S	41	T
+L	40	+	41	+	0M
+S	42	C
+L	41	+	42	+	0M
+S	43	G
+L	42	+	43	+	0M
+S	44	G
+L	43	+	44	+	0M
+S	71	C
+L	44	+	71	+	0M
+S	45	C
+L	44	+	45	+	0M
+L	71	+	45	+	0M
+S	46	A
+L	45	+	46	+	0M
+S	47	A
+L	46	+	47	+	0M
+S	48	T
+L	47	+	48	+	0M
+S	49	C
+L	48	+	49	+	0M
+S	50	C
+L	49	+	50	+	0M
+S	58	A
+L	49	+	58	+	0M
+S	51	A
+L	50	+	51	+	0M
+S	59	C
+L	58	+	59	+	0M
+S	86	G
+L	59	+	86	+	0M
+S	87	T
+L	86	+	87	+	0M
+P	1	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,24+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,50+,51+	*
+P	2	52+,53+,54+,1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,30+,31+,32+,33+,34+,35+,36+,55+,56+,57+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	3	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,60+,61+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	4	1+,2+,3+,4+,5+,6+,7+,62+,8+,9+,10+,63+,11+,12+,13+,14+,15+,16+,17+,18+,64+,65+,66+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	5	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,67+,68+,69+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	6	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,70+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,71+,45+,46+,47+,48+,49+,58+,59+	*
+P	7	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,72+,73+,74+,14+,15+,16+,17+,18+,19+,20+,21+,22+,75+,76+,23+,77+,26+,78+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	8	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,79+,80+,81+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+	*
+P	9	1+,2+,3+,4+,5+,6+,7+,82+,83+,10+,11+,12+,13+,15+,16+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	10	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,84+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,56+,57+,85+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+,86+,87+	*
+END
+
 	"$BINARY" -r4 ./test_data/seq.fa > out4.gfa
+	diff - out4.gfa << END
+H	VN:Z:1.0	NS:i:87	NL:i:109	NP:i:11
+S	52	C
+S	53	C
+L	52	+	53	+	0M
+S	54	A
+L	53	+	54	+	0M
+S	1	C
+L	54	+	1	+	0M
+S	2	G
+L	1	+	2	+	0M
+S	3	T
+L	2	+	3	+	0M
+S	4	C
+L	3	+	4	+	0M
+S	5	A
+L	4	+	5	+	0M
+S	6	A
+L	5	+	6	+	0M
+S	7	T
+L	6	+	7	+	0M
+S	62	G
+L	7	+	62	+	0M
+S	82	G
+L	7	+	82	+	0M
+S	8	C
+L	7	+	8	+	0M
+L	62	+	8	+	0M
+S	83	G
+L	82	+	83	+	0M
+S	9	T
+L	8	+	9	+	0M
+S	10	A
+L	9	+	10	+	0M
+L	83	+	10	+	0M
+S	63	G
+L	10	+	63	+	0M
+S	84	A
+L	10	+	84	+	0M
+S	11	T
+L	10	+	11	+	0M
+L	63	+	11	+	0M
+L	84	+	11	+	0M
+S	12	C
+L	11	+	12	+	0M
+S	13	G
+L	12	+	13	+	0M
+L	10	+	13	+	0M
+S	79	T
+L	12	+	79	+	0M
+S	72	G
+L	13	+	72	+	0M
+S	80	T
+L	79	+	80	+	0M
+S	73	T
+L	72	+	73	+	0M
+S	81	C
+L	80	+	81	+	0M
+S	74	A
+L	73	+	74	+	0M
+S	14	A
+L	13	+	14	+	0M
+L	74	+	14	+	0M
+L	81	+	14	+	0M
+S	15	A
+L	14	+	15	+	0M
+L	13	+	15	+	0M
+S	16	G
+L	15	+	16	+	0M
+S	17	C
+L	16	+	17	+	0M
+S	18	A
+L	17	+	18	+	0M
+S	64	G
+L	18	+	64	+	0M
+S	67	T
+L	18	+	67	+	0M
+S	65	C
+L	64	+	65	+	0M
+S	68	T
+L	67	+	68	+	0M
+S	66	T
+L	65	+	66	+	0M
+S	69	C
+L	68	+	69	+	0M
+S	19	T
+L	18	+	19	+	0M
+L	69	+	19	+	0M
+L	16	+	19	+	0M
+S	20	A
+L	19	+	20	+	0M
+S	21	C
+L	20	+	21	+	0M
+S	22	G
+L	21	+	22	+	0M
+L	66	+	22	+	0M
+S	75	C
+L	22	+	75	+	0M
+S	76	T
+L	75	+	76	+	0M
+S	23	C
+L	22	+	23	+	0M
+L	76	+	23	+	0M
+S	24	G
+L	23	+	24	+	0M
+S	77	T
+L	23	+	77	+	0M
+S	25	G
+L	24	+	25	+	0M
+L	23	+	25	+	0M
+S	26	G
+L	25	+	26	+	0M
+L	77	+	26	+	0M
+S	27	C
+L	26	+	27	+	0M
+S	78	T
+L	26	+	78	+	0M
+S	70	A
+L	27	+	70	+	0M
+S	28	A
+L	27	+	28	+	0M
+L	70	+	28	+	0M
+S	29	G
+L	28	+	29	+	0M
+S	30	A
+L	29	+	30	+	0M
+L	27	+	30	+	0M
+L	78	+	30	+	0M
+S	31	G
+L	30	+	31	+	0M
+S	32	C
+L	31	+	32	+	0M
+S	33	C
+L	32	+	33	+	0M
+S	60	C
+L	33	+	60	+	0M
+S	61	G
+L	60	+	61	+	0M
+S	34	G
+L	33	+	34	+	0M
+L	61	+	34	+	0M
+S	35	A
+L	34	+	35	+	0M
+S	36	A
+L	35	+	36	+	0M
+S	55	C
+L	36	+	55	+	0M
+S	56	T
+L	55	+	56	+	0M
+L	34	+	56	+	0M
+S	57	C
+L	56	+	57	+	0M
+S	37	G
+L	36	+	37	+	0M
+L	57	+	37	+	0M
+L	33	+	37	+	0M
+S	85	T
+L	57	+	85	+	0M
+S	38	A
+L	37	+	38	+	0M
+L	85	+	38	+	0M
+S	39	C
+L	38	+	39	+	0M
+S	40	C
+L	39	+	40	+	0M
+S	41	T
+L	40	+	41	+	0M
+S	42	C
+L	41	+	42	+	0M
+S	43	G
+L	42	+	43	+	0M
+S	44	G
+L	43	+	44	+	0M
+S	71	C
+L	44	+	71	+	0M
+S	45	C
+L	44	+	45	+	0M
+L	71	+	45	+	0M
+S	46	A
+L	45	+	46	+	0M
+S	47	A
+L	46	+	47	+	0M
+S	48	T
+L	47	+	48	+	0M
+S	49	C
+L	48	+	49	+	0M
+S	50	C
+L	49	+	50	+	0M
+S	58	A
+L	49	+	58	+	0M
+S	51	A
+L	50	+	51	+	0M
+S	59	C
+L	58	+	59	+	0M
+S	86	G
+L	59	+	86	+	0M
+S	87	T
+L	86	+	87	+	0M
+P	1	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,24+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,50+,51+	*
+P	2	52+,53+,54+,1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,30+,31+,32+,33+,34+,35+,36+,55+,56+,57+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	3	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,60+,61+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	4	1+,2+,3+,4+,5+,6+,7+,62+,8+,9+,10+,63+,11+,12+,13+,14+,15+,16+,17+,18+,64+,65+,66+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	5	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,67+,68+,69+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	6	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,70+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,71+,45+,46+,47+,48+,49+,58+,59+	*
+P	7	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,72+,73+,74+,14+,15+,16+,17+,18+,19+,20+,21+,22+,75+,76+,23+,77+,26+,78+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	8	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,79+,80+,81+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+	*
+P	9	1+,2+,3+,4+,5+,6+,7+,82+,83+,10+,11+,12+,13+,15+,16+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	10	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,84+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,56+,57+,85+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+,86+,87+	*
+P	Consensus_sequence	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+END
+
 	cp out.gfa in.gfa
 	cp out.msa in.msa
+
 	"$BINARY" -i in.gfa ./test_data/seq.fa -r3 > out.gfa
+	diff - out.gfa << END
+H	VN:Z:1.0	NS:i:87	NL:i:109	NP:i:20
+S	52	C
+S	53	C
+L	52	+	53	+	0M
+S	54	A
+L	53	+	54	+	0M
+S	1	C
+L	54	+	1	+	0M
+S	2	G
+L	1	+	2	+	0M
+S	3	T
+L	2	+	3	+	0M
+S	4	C
+L	3	+	4	+	0M
+S	5	A
+L	4	+	5	+	0M
+S	6	A
+L	5	+	6	+	0M
+S	7	T
+L	6	+	7	+	0M
+S	62	G
+L	7	+	62	+	0M
+S	82	G
+L	7	+	82	+	0M
+S	8	C
+L	7	+	8	+	0M
+L	62	+	8	+	0M
+S	83	G
+L	82	+	83	+	0M
+S	9	T
+L	8	+	9	+	0M
+S	10	A
+L	9	+	10	+	0M
+L	83	+	10	+	0M
+S	63	G
+L	10	+	63	+	0M
+S	84	A
+L	10	+	84	+	0M
+S	11	T
+L	10	+	11	+	0M
+L	63	+	11	+	0M
+L	84	+	11	+	0M
+S	12	C
+L	11	+	12	+	0M
+S	13	G
+L	12	+	13	+	0M
+L	10	+	13	+	0M
+S	79	T
+L	12	+	79	+	0M
+S	72	G
+L	13	+	72	+	0M
+S	80	T
+L	79	+	80	+	0M
+S	73	T
+L	72	+	73	+	0M
+S	81	C
+L	80	+	81	+	0M
+S	74	A
+L	73	+	74	+	0M
+S	14	A
+L	13	+	14	+	0M
+L	74	+	14	+	0M
+L	81	+	14	+	0M
+S	15	A
+L	14	+	15	+	0M
+L	13	+	15	+	0M
+S	16	G
+L	15	+	16	+	0M
+S	17	C
+L	16	+	17	+	0M
+S	18	A
+L	17	+	18	+	0M
+S	64	G
+L	18	+	64	+	0M
+S	67	T
+L	18	+	67	+	0M
+S	65	C
+L	64	+	65	+	0M
+S	68	T
+L	67	+	68	+	0M
+S	66	T
+L	65	+	66	+	0M
+S	69	C
+L	68	+	69	+	0M
+S	19	T
+L	18	+	19	+	0M
+L	69	+	19	+	0M
+L	16	+	19	+	0M
+S	20	A
+L	19	+	20	+	0M
+S	21	C
+L	20	+	21	+	0M
+S	22	G
+L	21	+	22	+	0M
+L	66	+	22	+	0M
+S	75	C
+L	22	+	75	+	0M
+S	76	T
+L	75	+	76	+	0M
+S	23	C
+L	22	+	23	+	0M
+L	76	+	23	+	0M
+S	24	G
+L	23	+	24	+	0M
+S	77	T
+L	23	+	77	+	0M
+S	25	G
+L	24	+	25	+	0M
+L	23	+	25	+	0M
+S	26	G
+L	25	+	26	+	0M
+L	77	+	26	+	0M
+S	27	C
+L	26	+	27	+	0M
+S	78	T
+L	26	+	78	+	0M
+S	70	A
+L	27	+	70	+	0M
+S	28	A
+L	27	+	28	+	0M
+L	70	+	28	+	0M
+S	29	G
+L	28	+	29	+	0M
+S	30	A
+L	29	+	30	+	0M
+L	27	+	30	+	0M
+L	78	+	30	+	0M
+S	31	G
+L	30	+	31	+	0M
+S	32	C
+L	31	+	32	+	0M
+S	33	C
+L	32	+	33	+	0M
+S	60	C
+L	33	+	60	+	0M
+S	61	G
+L	60	+	61	+	0M
+S	34	G
+L	33	+	34	+	0M
+L	61	+	34	+	0M
+S	35	A
+L	34	+	35	+	0M
+S	36	A
+L	35	+	36	+	0M
+S	55	C
+L	36	+	55	+	0M
+S	56	T
+L	55	+	56	+	0M
+L	34	+	56	+	0M
+S	57	C
+L	56	+	57	+	0M
+S	37	G
+L	36	+	37	+	0M
+L	57	+	37	+	0M
+L	33	+	37	+	0M
+S	85	T
+L	57	+	85	+	0M
+S	38	A
+L	37	+	38	+	0M
+L	85	+	38	+	0M
+S	39	C
+L	38	+	39	+	0M
+S	40	C
+L	39	+	40	+	0M
+S	41	T
+L	40	+	41	+	0M
+S	42	C
+L	41	+	42	+	0M
+S	43	G
+L	42	+	43	+	0M
+S	44	G
+L	43	+	44	+	0M
+S	71	C
+L	44	+	71	+	0M
+S	45	C
+L	44	+	45	+	0M
+L	71	+	45	+	0M
+S	46	A
+L	45	+	46	+	0M
+S	47	A
+L	46	+	47	+	0M
+S	48	T
+L	47	+	48	+	0M
+S	49	C
+L	48	+	49	+	0M
+S	50	C
+L	49	+	50	+	0M
+S	58	A
+L	49	+	58	+	0M
+S	51	A
+L	50	+	51	+	0M
+S	59	C
+L	58	+	59	+	0M
+S	86	G
+L	59	+	86	+	0M
+S	87	T
+L	86	+	87	+	0M
+P	1	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,24+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,50+,51+	*
+P	2	52+,53+,54+,1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,30+,31+,32+,33+,34+,35+,36+,55+,56+,57+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	3	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,60+,61+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	4	1+,2+,3+,4+,5+,6+,7+,62+,8+,9+,10+,63+,11+,12+,13+,14+,15+,16+,17+,18+,64+,65+,66+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	5	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,67+,68+,69+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	6	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,70+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,71+,45+,46+,47+,48+,49+,58+,59+	*
+P	7	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,72+,73+,74+,14+,15+,16+,17+,18+,19+,20+,21+,22+,75+,76+,23+,77+,26+,78+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	8	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,79+,80+,81+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+	*
+P	9	1+,2+,3+,4+,5+,6+,7+,82+,83+,10+,11+,12+,13+,15+,16+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	10	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,84+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,56+,57+,85+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+,86+,87+	*
+P	1	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,24+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,50+,51+	*
+P	2	52+,53+,54+,1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,30+,31+,32+,33+,34+,35+,36+,55+,56+,57+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	3	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,60+,61+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	4	1+,2+,3+,4+,5+,6+,7+,62+,8+,9+,10+,63+,11+,12+,13+,14+,15+,16+,17+,18+,64+,65+,66+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	5	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,14+,15+,16+,17+,18+,67+,68+,69+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	6	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,70+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,71+,45+,46+,47+,48+,49+,58+,59+	*
+P	7	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,13+,72+,73+,74+,14+,15+,16+,17+,18+,19+,20+,21+,22+,75+,76+,23+,77+,26+,78+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	8	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,11+,12+,79+,80+,81+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+	*
+P	9	1+,2+,3+,4+,5+,6+,7+,82+,83+,10+,11+,12+,13+,15+,16+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+	*
+P	10	1+,2+,3+,4+,5+,6+,7+,8+,9+,10+,84+,11+,12+,13+,14+,15+,16+,17+,18+,19+,20+,21+,22+,23+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34+,56+,57+,85+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,58+,59+,86+,87+	*
+END
+
 	"$BINARY" -i in.msa ./test_data/seq.fa -r1 > out.msa
+	diff - out.msa << END
+>1
+---CGTCAAT-CTA-TC--G---AAGCA---TACG--CGGGC-AGAGCC--GAA---GACCTCGG-CAATCCA--
+>2
+CCACGTCAAT-CTA-TC--G---AAGCA---TACG--C-GGC---AGCC--GAACTCGACCTCGG-CAATCAC--
+>3
+---CGTCAAT-CTA-TC--G---AAGCA---TACG--C-GGC-AGAGCCCGGAA---GACCTCGG-CAATCAC--
+>4
+---CGTCAATGCTAGTC--G---AAGCA---GCTG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATCAC--
+>5
+---CGTCAAT-CTA-TC--G---AAGCATTCTACG--C-GGC-AGAGCC--------GACCTCGG-CAATCAC--
+>6
+---CGTCAAT-CTA-----G---AAGCA---TACG--C-GGCAAGAGCC--GAA---GACCTCGGCCAATCAC--
+>7
+---CGTCAAT-CTA-TC--GGTAAAGCA---TACGCTC-TGT---AGCC--GAA---GACCTCGG-CAATCAC--
+>8
+---CGTCAAT-CTA-TCTTC---AAGCA---TACG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATC----
+>9
+---CGTCAAT-GGA-TC--G----AG-----TACG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATCAC--
+>10
+---CGTCAAT-CTAATC--G---AAGCA---TACG--C-GGC-AGAGCC--G---TCTACCTCGG-CAATCACGT
+>1
+---CGTCAAT-CTA-TC--G---AAGCA---TACG--CGGGC-AGAGCC--GAA---GACCTCGG-CAATCCA--
+>2
+CCACGTCAAT-CTA-TC--G---AAGCA---TACG--C-GGC---AGCC--GAACTCGACCTCGG-CAATCAC--
+>3
+---CGTCAAT-CTA-TC--G---AAGCA---TACG--C-GGC-AGAGCCCGGAA---GACCTCGG-CAATCAC--
+>4
+---CGTCAATGCTAGTC--G---AAGCA---GCTG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATCAC--
+>5
+---CGTCAAT-CTA-TC--G---AAGCATTCTACG--C-GGC-AGAGCC--------GACCTCGG-CAATCAC--
+>6
+---CGTCAAT-CTA-----G---AAGCA---TACG--C-GGCAAGAGCC--GAA---GACCTCGGCCAATCAC--
+>7
+---CGTCAAT-CTA-TC--GGTAAAGCA---TACGCTC-TGT---AGCC--GAA---GACCTCGG-CAATCAC--
+>8
+---CGTCAAT-CTA-TCTTC---AAGCA---TACG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATC----
+>9
+---CGTCAAT-GGA-TC--G----AG-----TACG--C-GGC-AGAGCC--GAA---GACCTCGG-CAATCAC--
+>10
+---CGTCAAT-CTAATC--G---AAGCA---TACG--C-GGC-AGAGCC--G---TCTACCTCGG-CAATCACGT
+END
+
 	"$BINARY" ./test_data/seq.fa -g poa.png > cons.fa
+	diff - cons.fa << END
+>Consensus_sequence
+CGTCAATCTATCGAAGCATACGCGGCAGAGCCGAAGACCTCGGCAATCAC
+END
+
 	"$BINARY" ./test_data/heter.fa -d2
 done