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

…tion Signed-off-by: Lydia Buntrock <[email protected]>
seqan · Aug 4, 2021 · 13f240a · 13f240a
1 parent 8b1569b
commit 13f240a
Show file tree

Hide file tree

Showing 8 changed files with 49 additions and 19 deletions.
diff --git a/test/cli/iGenVar_cli_test.cpp b/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';

diff --git a/test/data/datasources.cmake b/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=41f4591dd511406e5c3a79bf8e07af58110d03ad327592e4d8d6bdd8cbea7e10)
 
 # 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=5f2c89eb3aa4838e7c4ff9b2d08d0d715064f5e42e6851ecaddef4156e8e4655)
 
 # 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=a067034e05e8a39f3381c9cd2594d10fc8ccd74cf87069ab67ceb54de70b1693)
diff --git a/test/data/mini_example/explanation.fasta b/test/data/mini_example/explanation.fasta
@@ -1,25 +1,29 @@
 >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: novel element inserted after 125
+ACGCCGGGAATCGGTAGTCCTTTCGCGGGG ATATATTT ATATATTT TACGGGATATAA <- Tandem Duplication   ref: (180, 188] tandem duplicated
 CGATCGGATCGGATCGATAATAGGTCTCGGTTGCCAACTGATCGTACCAA
-ATATTTCTGCGGGGCT TCGGCTAACGGTT AGAG CGCCCCTCCGCGATTA C              <- Translocation    ref: (266, 267, 232, 233, 236, 237, 249)
-                                                                                oder    ref: [267, 286] deleted
-ACCCATGCGGATTATAAACGGG ATATTAAGGGCTTT                               <- Duplication in der Referenz
-AGGGCTAGCTAGGTCCAA
+ATATTTCTGCGGGGCT TCGGCTAACGGTT AGAG CGCCCCTCCGCGATTA C        <- Double Translocation ref: (266, 282] translocated after 286
+                                                                                   or ref: (286, 299] translocated after 266
+ACCCATGCGGATTATAAACGGG ATATTAAGGGCTTT                         <- Duplication in the   ref: maps to (322, 336] & (336, 350]
+AGGGCTAGCTAGGTCCAA GGTAACGTGTA AGCTTTCGGAACGTAC   CGGTA       <- Translocation        ref: (368, 384] translocated after 395
+CGTACTGAAAAAAACCAAACGGGGAAATATTAACCGGCCTTTGCCTGGGA
+CGCTGTGACTGTACGGGGGGG ACTAGCGATGCTAGCTAGCTAGCT CGGGCCTTATT    <- Duplication          ref: (10, 34] duplicated after 471
 
->insertion
+>novel_element_insertion
 CCCCGGGGCCAATTT
 
 2048: split reads

diff --git a/test/data/mini_example/mini_example_reference.fasta b/test/data/mini_example/mini_example_reference.fasta
@@ -6,4 +6,6 @@ ACGCCGGGAATCGGTAGTCCTTTCGCGGGGATATATTTTACGGGATATAA
 CGATCGGATCGGATCGATAATAGGTCTCGGTTGCCAACTGATCGTACCAA
 ATATTTCTGCGGGGCTCGCCCCTCCGCGATTAAGAGTCGGCTAACGGTTC
 ACCCATGCGGATTATAAACGGGATATTAAGGGCTTTATATTAAGGGCTTT
-AGGGCTAGCTAGGTCCAA
+AGGGCTAGCTAGGTCCAAAGCTTTCGGAACGTACGGTAACGTGTACGGTA
+CGTACTGAAAAAAACCAAACGGGGAAATATTAACCGGCCTTTGCCTGGGA
+CGCTGTGACTGTACGGGGGGGCGGGCCTTATT
diff --git a/test/data/mini_example/output_err.txt b/test/data/mini_example/output_err.txt
@@ -33,6 +33,15 @@ 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
+INS: chr1	367	Forward	chr1	368	Forward	11	read046
+INS: chr1	367	Forward	chr1	368	Forward	11	read047
+INS: chr1	367	Forward	chr1	368	Forward	11	read048
+INS: chr1	367	Forward	chr1	368	Forward	11	read049
+INS: chr1	367	Forward	chr1	368	Forward	11	read050
+DEL: chr1	383	Forward	chr1	395	Forward	0	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 15 junction clusters.
 No refinement was selected.
diff --git a/test/data/mini_example/output_res.txt b/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	<INS>	5	PASS	END=368;SVLEN=11;SVTYPE=INS	GT	./.
+chr1	384	.	N	<DEL>	1	PASS	END=395;SVLEN=-11;SVTYPE=DEL	GT	./.
diff --git a/test/data/mini_example/single_end_IGV_View.png b/test/data/mini_example/single_end_IGV_View.png
diff --git a/test/data/mini_example/single_end_mini_example.sam b/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 +72,13 @@ 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	32M11I7M	*	0	0	ATATTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTC	*	AS:i:35	NM:i:16
+read047	0	chr1	338	60	31M11I8M	*	0	0	TATTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCG	*	AS:i:35	NM:i:16
+read048	0	chr1	339	60	30M11I9M	*	0	0	ATTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGG	*	AS:i:35	NM:i:16
+read049	0	chr1	340	60	29M11I10M	*	0	0	TTAAGGGCTTTAGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGGA	*	AS:i:35	NM:i:16
+read050	0	chr1	351	60	18M11I16M11D5M	*	0	0	AGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGGAACGTACCGGTA	*	AS:i:40	NM:i:11
+read050	256	chr1	351	60	18M11I16M5S	*	0	0	AGGGCTAGCTAGGTCCAAGGTAACGTGTAAGCTTTCGGAACGTACCGGTA	*	AS:i:35	NM:i:0
+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