[TEST] Add more test cases to mini example: Translocation and Duplica…

…tion

Signed-off-by: Lydia Buntrock <[email protected]>

test/cli/iGenVar_cli_test.cpp

@@ -526,7 +526,8 @@ TEST_F(iGenVar_cli_test, dataset_single_end_mini_example)
 {
     cli_test_result result = execute_app("iGenVar",
                                          "-j", data("single_end_mini_example.sam"),
-                                         "--method cigar_string --method split_read --min_var_length 8");
+                                         "--method cigar_string --method split_read "
+                                         "--min_var_length 8 --max_var_length 400");
 
     // Check the output of junctions:
     seqan3::debug_stream << "Check the output of junctions... " << '\n';

test/data/datasources.cmake

@@ -19,14 +19,14 @@ declare_datasource (FILE paired_end_mini_example.sam
 # copies file to <build>/data/single_end_mini_example.sam
 declare_datasource (FILE single_end_mini_example.sam
                     URL ${CMAKE_SOURCE_DIR}/test/data/mini_example/single_end_mini_example.sam
-                    URL_HASH SHA256=ea89fb00c802e5136ca8dd32362648c8192652a34078bfa25b8ae78695a27cd6)
+                    URL_HASH SHA256=14ed3cc5517c33530761b13b3a474eb85de8c0ec00c07702430530f860867a10)
 
 # copies file to <build>/data/output_err.txt
 declare_datasource (FILE output_err.txt
                     URL ${CMAKE_SOURCE_DIR}/test/data/mini_example/output_err.txt
-                    URL_HASH SHA256=415171afbdf18cffef58599af346b73208457f4406343cf5e69a1d125b4a9c02)
+                    URL_HASH SHA256=3f11dedb02d5493536b38adc2d12a6e69704ba7a7701befdf2c369ffdbf4b3ee)
 
 # copies file to <build>/data/output_res.txt
 declare_datasource (FILE output_res.txt
                     URL ${CMAKE_SOURCE_DIR}/test/data/mini_example/output_res.txt
-                    URL_HASH SHA256=1b9e3c3f2e7d599b50370bdfb16d41d485c5efdf5ceb2b63e17fc69c40ec71dc)
+                    URL_HASH SHA256=93c7fe1e0ae0d44b4d6dddc63b5c71915ee31b3ce1a1934ff9424efe6da4676e)

test/data/mini_example/explanation.fasta

@@ -1,23 +1,28 @@
 >ref
-CGCCCATGCAACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCG
+CGCCCATGCA ACTAGCGATGCTAGCTAGCTAGCT TACGACTGGCCATGCG
 GCGGCAT ATTTATAACGGGC ATACATAAGGGGCTCATCGATCGATTTCGG
 ATCGGGGGGCCCCCATTTTAAACGG   GGATCTTGACTCTGGAAAACTTTTA
 ACGCCGGGAATCGGTAGTCCTTTCGCGGGG ATATATTT TACGGGATATAA
 CGATCGGATCGGATCGATAATAGGTCTCGGTTGCCAACTGATCGTACCAA
 ATATTTCTGCGGGGCT   CGCCCCTCCGCGATTA AGAG TCGGCTAACGGTT C
 ACCCATGCGGATTATAAACGGG ATATTAAGGGCTTT ATATTAAGGGCTTT
-AGGGCTAGCTAGGTCCAA
+AGGGCTAGCTAGGTCCAA   AGCTTTCGGAACGTAC GGTAACGTGTA CGGTA
+CGTACTGAAAAAAACCAAACGGGGAAATATTAACCGGCCTTTGCCTGGGA
+CGCTGTGACTGTACGGGGGGGCGGGCCTTATT
 
 >new_Creature
-CGCCCATGCAACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCG                                      breakpoints:
-GCGGCAT ATACATAAGGGGCTCATCGATCGATTTCGG                              <- Deletion         ref: [57, 70] deleted
-ATCGGGGGGCCCCCATTTTAAACGG CCCCGGGGCCAATTT GGATCTTGACTCTGGAAAACTTTTA <- Insertion        ref: after 125 something inserted
-ACGCCGGGAATCGGTAGTCCTTTCGCGGGG ATATATTT ATATATTT TACGGGATATAA       <- Duplication      ref: (180 or 189) something inserted
+CGCCCATGCAACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCG                                          breakpoints:
+GCGGCAT ATACATAAGGGGCTCATCGATCGATTTCGG                              <- Deletion             ref: (57, 70] deleted
+ATCGGGGGGCCCCCATTTTAAACGG CCCCGGGGCCAATTT GGATCTTGACTCTGGAAAACTTTTA <- Insertion            ref: after 125
+ACGCCGGGAATCGGTAGTCCTTTCGCGGGG ATATATTT ATATATTT TACGGGATATAA       <- Tandem Duplication   ref: [180, 188] duplicated
 CGATCGGATCGGATCGATAATAGGTCTCGGTTGCCAACTGATCGTACCAA
-ATATTTCTGCGGGGCT TCGGCTAACGGTT AGAG CGCCCCTCCGCGATTA C              <- Translocation    ref: (266, 267, 232, 233, 236, 237, 249)
-                                                                                oder    ref: [267, 286] deleted
+ATATTTCTGCGGGGCT TCGGCTAACGGTT AGAG CGCCCCTCCGCGATTA C              <- Double Translocation ref: (266, 267, 232, 233, 236, 237, 249)
+                                                                                oder        ref: [267, 286] deleted
 ACCCATGCGGATTATAAACGGG ATATTAAGGGCTTT                               <- Duplication in der Referenz
-AGGGCTAGCTAGGTCCAA
+AGGGCTAGCTAGGTCCAA GGTAACGTGTA AGCTTTCGGAACGTAC   CGGTA             <- Translocation        deletion - ref: (368, 384]
+CGTACTGAAAAAAACCAAACGGGGAAATATTAACCGGCCTTTGCCTGGGA                                          + insertion - ref: after 395
+CGCTGTGACTGTACGGGGGGG ACTAGCGATGCTAGCTAGCTAGCT CGGGCCTTATT          <- Duplication          ref: after 471
+                                                                                            -> inserted sequence from ref: (10, 34]
 
 >insertion
 CCCCGGGGCCAATTT

test/data/mini_example/mini_example_reference.fasta

@@ -6,4 +6,6 @@ ACGCCGGGAATCGGTAGTCCTTTCGCGGGGATATATTTTACGGGATATAA
 CGATCGGATCGGATCGATAATAGGTCTCGGTTGCCAACTGATCGTACCAA
 ATATTTCTGCGGGGCTCGCCCCTCCGCGATTAAGAGTCGGCTAACGGTTC
 ACCCATGCGGATTATAAACGGGATATTAAGGGCTTTATATTAAGGGCTTT
-AGGGCTAGCTAGGTCCAA
+AGGGCTAGCTAGGTCCAAAGCTTTCGGAACGTACGGTAACGTGTACGGTA
+CGTACTGAAAAAAACCAAACGGGGAAATATTAACCGGCCTTTGCCTGGGA
+CGCTGTGACTGTACGGGGGGGCGGGCCTTATT

test/data/mini_example/output_err.txt

@@ -33,6 +33,19 @@ DEL: chr1	335	Forward	chr1	350	Forward	0	read042
 DEL: chr1	335	Forward	chr1	350	Forward	0	read043
 DEL: chr1	335	Forward	chr1	350	Forward	0	read044
 DEL: chr1	335	Forward	chr1	350	Forward	0	read045
+DEL: chr1	367	Forward	chr1	384	Forward	0	read046
+BND: chr1	368	Reverse	chr1	394	Reverse	0	read046
+DEL: chr1	367	Forward	chr1	384	Forward	0	read047
+BND: chr1	368	Reverse	chr1	394	Reverse	0	read047
+DEL: chr1	367	Forward	chr1	384	Forward	0	read048
+BND: chr1	368	Reverse	chr1	394	Reverse	0	read048
+DEL: chr1	367	Forward	chr1	384	Forward	0	read049
+BND: chr1	368	Reverse	chr1	394	Reverse	0	read049
+DEL: chr1	367	Forward	chr1	384	Forward	0	read050
+INS: chr1	394	Forward	chr1	395	Forward	16	read050
+BND: chr1	10	Reverse	chr1	470	Reverse	0	read051
+BND: chr1	10	Reverse	chr1	470	Reverse	0	read052
+BND: chr1	33	Forward	chr1	471	Forward	0	read052
 Start clustering...
-Done with clustering. Found 11 junction clusters.
+Done with clustering. Found 16 junction clusters.
 No refinement was selected.

test/data/mini_example/output_res.txt

@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##source=iGenVarCaller
-##contig=<ID=chr1,length=368>
+##contig=<ID=chr1,length=482>
 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of SV called.",Source="iGenVarCaller",Version="1.0">
 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of SV called.",Source="iGenVarCaller",Version="1.0">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of SV called.",Source="iGenVarCaller",Version="1.0">
@@ -13,3 +13,5 @@ chr1	180	.	N	<INS>	1	PASS	END=180;SVLEN=8;SVTYPE=INS	GT	./.
 chr1	266	.	N	<DEL>	4	PASS	END=286;SVLEN=-20;SVTYPE=DEL	GT	./.
 chr1	282	.	N	<DEL>	1	PASS	END=299;SVLEN=-17;SVTYPE=DEL	GT	./.
 chr1	336	.	N	<DEL>	4	PASS	END=350;SVLEN=-14;SVTYPE=DEL	GT	./.
+chr1	368	.	N	<DEL>	5	PASS	END=384;SVLEN=-16;SVTYPE=DEL	GT	./.
+chr1	395	.	N	<INS>	1	PASS	END=395;SVLEN=16;SVTYPE=INS	GT	./.

test/data/mini_example/single_end_mini_example.sam

@@ -1,5 +1,5 @@
 @HD	VN:1.6	SO:coordinate
-@SQ	SN:chr1	LN:368
+@SQ	SN:chr1	LN:482
 read001	0	chr1	1	60	50M	*	0	0	CGCCCATGCAACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCG	*	AS:i:50	NM:i:0
 read002	0	chr1	2	60	50M	*	0	0	GCCCATGCAACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCGG	*	AS:i:50	NM:i:0
 read003	0	chr1	3	60	50M	*	0	0	CCCATGCAACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCGGC	*	AS:i:50	NM:i:0
@@ -11,6 +11,8 @@ read008	0	chr1	8	60	50M	*	0	0	GCAACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCGGCGGCAT
 read009	0	chr1	9	60	49M1S	*	0	0	CAACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCGGCGGCATA	*	AS:i:49	NM:i:0
 read010	0	chr1	10	60	48M13D2M	*	0	0	AACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCGGCGGCATAT	*	AS:i:46	NM:i:13
 read011	0	chr1	11	60	47M13D3M	*	0	0	ACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCGGCGGCATATA	*	AS:i:46	NM:i:13
+read051	2048	chr1	11	60	27S23M	*	0	0	CTGGGACGCTGTGACTGTACGGGGGGGACTAGCGATGCTAGCTAGCTAGC	*	AS:i:23	NM:i:0
+read052	2048	chr1	11	60	21S24M5S	*	0	0	CGCTGTGACTGTACGGGGGGGACTAGCGATGCTAGCTAGCTAGCTCGGGC	*	AS:i:24	NM:i:0
 read012	0	chr1	12	60	46M13D4M	*	0	0	CTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCGGCGGCATATAC	*	AS:i:46	NM:i:13
 read013	0	chr1	51	60	7M13D43M	*	0	0	GCGGCATATACATAAGGGGCTCATCGATCGATTTCGGATCGGGGGGCCCC	*	AS:i:46	NM:i:13
 read014	0	chr1	52	60	6M13D44M	*	0	0	CGGCATATACATAAGGGGCTCATCGATCGATTTCGGATCGGGGGGCCCCC	*	AS:i:46	NM:i:13
@@ -70,3 +72,18 @@ read044	0	chr1	303	60	34M14D16M	*	0	0	CCATGCGGATTATAAACGGGATATTAAGGGCTTTAGGGCTAG
 read044	256	chr1	303	60	20M14D30M	*	0	0	CCATGCGGATTATAAACGGGATATTAAGGGCTTTAGGGCTAGCTAGGTCC	*	AS:i:46	NM:i:14
 read045	0	chr1	305	60	32M14D18M	*	0	0	ATGCGGATTATAAACGGGATATTAAGGGCTTTAGGGCTAGCTAGGTCCAA	*	AS:i:46	NM:i:14
 read045	256	chr1	305	60	18M14D32M	*	0	0	ATGCGGATTATAAACGGGATATTAAGGGCTTTAGGGCTAGCTAGGTCCAA	*	AS:i:46	NM:i:14
+read046	0	chr1	337	60	32M16D11M7S	*	0	0	ATATTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTC	*	AS:i:38	NM:i:16	SA:Z:chr1,369,+,43S7M,60,0;
+read047	0	chr1	338	60	31M16D11M8S	*	0	0	TATTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCG	*	AS:i:37	NM:i:16	SA:Z:chr1,369,+,42S8M,60,0;
+read048	0	chr1	339	60	30M16D11M9S	*	0	0	ATTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGG	*	AS:i:36	NM:i:16	SA:Z:chr1,369,+,41S9M,60,0;
+read049	0	chr1	340	60	29M16D11M10S	*	0	0	TTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGGA	*	AS:i:35	NM:i:16	SA:Z:chr1,369,+,40S10M,60,0;
+read050	0	chr1	351	60	18M16D11M16I5M	*	0	0	AGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGGAACGTACCGGTA	*	AS:i:25	NM:i:32
+read050	256	chr1	351	60	18M16D11M21S	*	0	0	AGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGGAACGTACCGGTA	*	AS:i:24	NM:i:16
+read046	2048	chr1	369	60	43S7M	*	0	0	ATATTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTC	*	AS:i:7	NM:i:0
+read047	2048	chr1	369	60	42S8M	*	0	0	TATTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCG	*	AS:i:8	NM:i:0
+read048	2048	chr1	369	60	41S9M	*	0	0	ATTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGG	*	AS:i:9	NM:i:0
+read049	2048	chr1	369	60	40S10M	*	0	0	TTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGGA	*	AS:i:10	NM:i:0
+read050	2304	chr1	369	60	29S16M16D5M	*	0	0	AGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGGAACGTACCGGTA	*	AS:i:16	NM:i:16
+read051	0	chr1	445	60	27M23S	*	0	0	CTGGGACGCTGTGACTGTACGGGGGGGACTAGCGATGCTAGCTAGCTAGC	*	AS:i:27	NM:i:0	SA:Z:chr1,11,+,27S23M,60,0;
+read052	0	chr1	451	60	21M29S	*	0	0	CGCTGTGACTGTACGGGGGGGACTAGCGATGCTAGCTAGCTAGCTCGGGC	*	AS:i:24	NM:i:0	SA:Z:chr1,11,+,21S24M5S,60,0;chr1,472,+,45S5M,60,0;
+read052	256	chr1	451	60	21M24I5M	*	0	0	CGCTGTGACTGTACGGGGGGGACTAGCGATGCTAGCTAGCTAGCTCGGGC	*	AS:i:21	NM:i:0
+read052	2048	chr1	472	60	45S5M	*	0	0	CGCTGTGACTGTACGGGGGGGACTAGCGATGCTAGCTAGCTAGCTCGGGC	*	AS:i:24	NM:i:0