added VCF to init golden-test

.gitignore

@@ -1,3 +1,4 @@
 docs/_build/
 .stack-work/
-dist-newstyle/
+dist-newstyle/
+.DS_Store

test/PoseidonGoldenTests/GoldenTestCheckSumFile.txt

@@ -7,6 +7,10 @@ fd632717ecaf337a39cfd7a828a54e99 init init/Schiffels/Schiffels.janno
 9edc4a757f785a8ecb59c54d16c5690a init init/Schiffels/Schiffels.bib
 c35421d9be15aa66fa3a3c46df1f746c init init/Wang/POSEIDON.yml
 ae66d851301f4a761b819f97ec28fa55 init init/Wang/Wang_2020.bed
+956c7bf4c6999cc322ad8407d8bef776 init init_vcf/Schiffels_vcf/POSEIDON.yml
+02386e2064f92c68d4be8fea2e2f923c init init_vcf/Schiffels_vcf/Schiffels.janno
+b60795356b27b5e35002e44fcb24b0a7 init init_vcf/Schiffels_vcf/geno.vcf
+9edc4a757f785a8ecb59c54d16c5690a init init_vcf/Schiffels_vcf/Schiffels.bib
 d41d8cd98f00b204e9800998ecf8427e validate validate/validate1
 d41d8cd98f00b204e9800998ecf8427e validate validate/validate2
 d41d8cd98f00b204e9800998ecf8427e validate validate/validate3

test/PoseidonGoldenTests/GoldenTestData/chronicle/chronicle2.yml

@@ -1,29 +1,29 @@
 title: Chronicle title
 description: Chronicle description
 chronicleVersion: 0.2.0
-lastModified: 2024-09-06
+lastModified: 2024-10-25
 packages:
 - title: Lamnidis_2018
   version: 1.0.0
-  commit: d0e37c0d599600ee2c81d1b75cdcbb0316c2b60c
+  commit: 7905674f72b3336111507881e87dfd477bbe7780
   path: Lamnidis_2018
 - title: Lamnidis_2018
   version: 1.0.1
-  commit: d0e37c0d599600ee2c81d1b75cdcbb0316c2b60c
+  commit: 7905674f72b3336111507881e87dfd477bbe7780
   path: Lamnidis_2018_newVersion
 - title: Schiffels
   version: 1.1.1
-  commit: 14c6c1e40f778d49202e334ebb5eab5b827405ba
+  commit: c7cbb379df193c005afc70edc17fbb5b12df17fa
   path: Schiffels
 - title: Schiffels_2016
   version: 1.0.1
-  commit: d0e37c0d599600ee2c81d1b75cdcbb0316c2b60c
+  commit: 7905674f72b3336111507881e87dfd477bbe7780
   path: Schiffels_2016
 - title: Schmid_2028
   version: 1.0.0
-  commit: d0e37c0d599600ee2c81d1b75cdcbb0316c2b60c
+  commit: 7905674f72b3336111507881e87dfd477bbe7780
   path: Schmid_2028
 - title: Wang_2020
   version: 0.1.0
-  commit: d0e37c0d599600ee2c81d1b75cdcbb0316c2b60c
+  commit: 7905674f72b3336111507881e87dfd477bbe7780
   path: Wang_2020

test/PoseidonGoldenTests/GoldenTestData/init_vcf/Schiffels_vcf/POSEIDON.yml

@@ -0,0 +1,10 @@
+poseidonVersion: 2.7.1
+title: Schiffels
+description: Empty package template. Please add a description
+packageVersion: 0.1.0
+lastModified: 1970-01-01
+genotypeData:
+  format: VCF
+  genoFile: geno.vcf
+jannoFile: Schiffels.janno
+bibFile: Schiffels.bib

test/PoseidonGoldenTests/GoldenTestData/init_vcf/Schiffels_vcf/Schiffels.bib

@@ -0,0 +1,12 @@
+@article{exampleBibtexKey,
+  title = {Example Paper},
+  author = {Doe, John},
+  year = {2018},
+  journal = {Example Journal},
+  volume = {47},
+  issue = {10},
+  publisher = {The example society for example research},
+  doi = {10.XXXX/ExampleJournal.47.777},
+  url = {https://doi.org/10.XXXX/ExampleJournal.47.777},
+}
+

test/PoseidonGoldenTests/GoldenTestData/init_vcf/Schiffels_vcf/Schiffels.janno

@@ -0,0 +1,11 @@
+Poseidon_ID	Genetic_Sex	Group_Name	Alternative_IDs	Relation_To	Relation_Degree	Relation_Type	Relation_Note	Collection_ID	Country	Country_ISO	Location	Site	Latitude	Longitude	Date_Type	Date_C14_Labnr	Date_C14_Uncal_BP	Date_C14_Uncal_BP_Err	Date_BC_AD_Start	Date_BC_AD_Median	Date_BC_AD_Stop	Date_Note	MT_Haplogroup	Y_Haplogroup	Source_Tissue	Nr_Libraries	Library_Names	Capture_Type	UDG	Library_Built	Genotype_Ploidy	Data_Preparation_Pipeline_URL	Endogenous	Nr_SNPs	Coverage_on_Target_SNPs	Damage	Contamination	Contamination_Err	Contamination_Meas	Contamination_Note	Genetic_Source_Accession_IDs	Primary_Contact	Publication	Note	Keywords
+XXX001	U	unknown	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a
+XXX002	U	unknown	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a
+XXX003	U	unknown	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a
+XXX004	U	unknown	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a
+XXX005	U	unknown	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a
+XXX006	U	unknown	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a
+XXX007	U	unknown	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a
+XXX008	U	unknown	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a
+XXX009	U	unknown	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a
+XXX010	U	unknown	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a

test/PoseidonGoldenTests/GoldenTestData/init_vcf/Schiffels_vcf/geno.vcf

@@ -0,0 +1,11 @@
+##fileformat=VCFv4.2
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XXX001	XXX002	XXX003	XXX004	XXX005	XXX006	XXX007	XXX008	XXX009	XXX010
+1	752566	1_752566	G	A	0	.	.	GT	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1
+1	842013	1_842013	T	G	0	.	.	GT	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
+1	891021	1_891021	G	A	0	.	.	GT	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1
+1	949654	1_949654	A	G	0	.	.	GT	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1
+2	1018704	2_1018704	A	G	0	.	.	GT	0/1	0/1	0/0	0/1	./.	1/1	0/1	0/0	1/1	0/1
+2	1045331	2_1045331	G	A	0	.	.	GT	1/1	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0
+2	1048955	2_1048955	A	G	0	.	.	GT	1/1	1/1	./.	1/1	0/0	0/0	0/1	0/0	0/0	0/1 
+2	1061166	2_1061166	T	C	0	.	.	GT	0/0	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/0	1/1
+2	1108637	2_1108637	G	A	0	.	.	GT	0/0	0/0	./.	1/1	0/1	0/0	0/0	0/0	0/1	0/0

test/PoseidonGoldenTests/GoldenTestsRunCommands.hs

@@ -81,6 +81,8 @@ dynamicCheckSumFile :: FilePath
 dynamicCheckSumFile = "/tmp/poseidon_trident_dynamicCheckSumFile.txt"
 testPacsDir         :: FilePath
 testPacsDir         = "test/testDat/testPackages/ancient"
+testPacsDirOther    :: FilePath
+testPacsDirOther    = "test/testDat/testPackages/other_test_packages"
 testEntityFiles     :: FilePath
 testEntityFiles     = "test/testDat/testEntityFiles"
 
@@ -225,6 +227,7 @@ testPipelineInit testDir checkFilePath = do
         , "init" </> "Schiffels" </> "geno.txt"
         , "init" </> "Schiffels" </> "Schiffels.bib"
         ]
+
     let initOpts2 = InitOptions {
           _initGenoData  = GenotypeDataSpec {
             genotypeFileSpec = GenotypePlink {
@@ -247,6 +250,28 @@ testPipelineInit testDir checkFilePath = do
           "init" </> "Wang" </> "POSEIDON.yml"
         , "init" </> "Wang" </> "Wang_2020.bed"
         ]
+
+    let initOpts3 = InitOptions {
+          _initGenoData  = GenotypeDataSpec {
+              genotypeFileSpec = GenotypeVCF {
+                _vcfGenoFile = testPacsDirOther </> "Schiffels_2016_vcf" </> "geno.vcf"
+              , _vcfGenoFileChkSum = Nothing
+              }
+            , genotypeSnpSet   = Just SNPSetOther
+            }
+        , _initPacPath      = testDir </> "init_vcf" </> "Schiffels_vcf"
+        , _initPacName      = Just "Schiffels"
+        , _initMinimal      = False
+    }
+    let action3 = testLog (runInit initOpts3) >>
+                 patchLastModified testDir ("init_vcf" </> "Schiffels_vcf" </> "POSEIDON.yml")
+    runAndChecksumFiles checkFilePath testDir action3 "init" [
+          "init_vcf" </> "Schiffels_vcf" </> "POSEIDON.yml"
+        , "init_vcf" </> "Schiffels_vcf" </> "Schiffels.janno"
+        , "init_vcf" </> "Schiffels_vcf" </> "geno.vcf"
+        , "init_vcf" </> "Schiffels_vcf" </> "Schiffels.bib"
+        ]
+
 
 testPipelineValidate :: FilePath -> FilePath -> IO ()
 testPipelineValidate testDir checkFilePath = do
@@ -404,6 +429,7 @@ testPipelineGenoconvert testDir checkFilePath = do
         , "genoconvert" </> "Schiffels" </> "Schiffels_2016.bim"
         , "genoconvert" </> "Schiffels" </> "Schiffels_2016.fam"
         ]
+
     let genoconvertOpts2 = GenoconvertOptions {
           _genoconvertGenoSources = [PacBaseDir $ testPacsDir </> "Schiffels_2016"]
         , _genoConvertOutFormat = "PLINK"
@@ -418,6 +444,7 @@ testPipelineGenoconvert testDir checkFilePath = do
         , "genoconvert" </> "Schiffels_otherPlinkEncoding" </> "Schiffels_2016.bim"
         , "genoconvert" </> "Schiffels_otherPlinkEncoding" </> "Schiffels_2016.fam"
         ]
+
     -- in-place conversion
     let genoconvertOpts3 = GenoconvertOptions {
           _genoconvertGenoSources = [PacBaseDir $ testDir </> "init" </> "Wang"]
@@ -433,6 +460,7 @@ testPipelineGenoconvert testDir checkFilePath = do
         , "init" </> "Wang" </> "Wang.snp"
         , "init" </> "Wang" </> "Wang.ind"
         ]
+
     let genoconvertOpts4 = GenoconvertOptions {
           _genoconvertGenoSources = [
             GenoDirect $
@@ -460,6 +488,30 @@ testPipelineGenoconvert testDir checkFilePath = do
         , "init" </> "Schiffels" </> "geno.bim"
         , "init" </> "Schiffels" </> "geno.fam"
         ]
+
+    -- let genoconvertOpts5 = GenoconvertOptions {
+    --       _genoconvertGenoSources = [
+    --         GenoDirect $
+    --           GenotypeDataSpec {
+    --               genotypeFileSpec = GenotypeVCF {
+    --                 _vcfGenoFile = testDir </> "init" </> "Schiffels_vcf" </> "geno.vcf"
+    --               , _vcfGenoFileChkSum = Nothing
+    --             }
+    --             , genotypeSnpSet   = Just SNPSetOther
+    --           }
+    --       ]
+    --     , _genoConvertOutFormat = "PLINK"
+    --     , _genoConvertOutOnlyGeno = True
+    --     , _genoMaybeOutPackagePath = Nothing
+    --     , _genoconvertRemoveOld = False
+    --     , _genoconvertOutPlinkPopMode = PlinkPopNameAsFamily
+    --     , _genoconvertOnlyLatest = False
+    -- }
+    -- runAndChecksumFiles checkFilePath testDir (testLog $ runGenoconvert genoconvertOpts5) "genoconvert" [
+    --       "init" </> "Schiffels_vcf" </> "geno.bed"
+    --     , "init" </> "Schiffels_vcf" </> "geno.bim"
+    --     , "init" </> "Schiffels_vcf" </> "geno.fam"
+    --     ]
 
 testPipelineRectify :: FilePath -> FilePath -> IO ()
 testPipelineRectify testDir checkFilePath = do

test/testDat/.gitignore

@@ -1,2 +1,2 @@
 poseidonHSGoldenTestData/2019_Nikitin_LBK/*.bed
-poseidonHSGoldenTestData/2019_Nikitin_LBK/*.bim
+poseidonHSGoldenTestData/2019_Nikitin_LBK/*.bim