finished removing onlyGeno option

poseidon-framework · Nov 22, 2024 · 2499894 · 2499894
1 parent 3e8bc07
commit 2499894
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 9 deletions.
diff --git a/src/Poseidon/CLI/Genoconvert.hs b/src/Poseidon/CLI/Genoconvert.hs
@@ -79,7 +79,7 @@ convertGenoTo outFormat onlyGeno outPath removeOld outPlinkPopMode outZip pac =
 
     -- compile new relative file names
     let outName = getPacName . posPacNameAndVersion $ pac
-    let gz = "gz"
+    let gz = if outZip then "gz" else ""
     (outIrel, outSrel, outGrel) <- case outFormat of
             "EIGENSTRAT" -> return
                 (outName <.> ".ind", outName <.> ".snp" <.> gz, outName <.> ".geno" <.> gz)

diff --git a/test/PoseidonGoldenTests/GoldenTestsRunCommands.hs b/test/PoseidonGoldenTests/GoldenTestsRunCommands.hs
@@ -417,7 +417,6 @@ testPipelineGenoconvert testDir checkFilePath = do
     let genoconvertOpts1 = GenoconvertOptions {
           _genoconvertGenoSources = [PacBaseDir $ testPacsDir </> "Schiffels_2016"]
         , _genoConvertOutFormat = "PLINK"
-        , _genoConvertOutOnlyGeno = False
         , _genoMaybeOutPackagePath = Just $ testDir </> "genoconvert" </> "Schiffels"
         , _genoconvertRemoveOld = False
         , _genoconvertOutPlinkPopMode = PlinkPopNameAsFamily
@@ -433,7 +432,6 @@ testPipelineGenoconvert testDir checkFilePath = do
     let genoconvertOpts2 = GenoconvertOptions {
           _genoconvertGenoSources = [PacBaseDir $ testPacsDir </> "Schiffels_2016"]
         , _genoConvertOutFormat = "PLINK"
-        , _genoConvertOutOnlyGeno = False
         , _genoMaybeOutPackagePath = Just $ testDir </> "genoconvert" </> "Schiffels_otherPlinkEncoding"
         , _genoconvertRemoveOld = False
         , _genoconvertOutPlinkPopMode = PlinkPopNameAsPhenotype
@@ -450,7 +448,6 @@ testPipelineGenoconvert testDir checkFilePath = do
     let genoconvertOpts3 = GenoconvertOptions {
           _genoconvertGenoSources = [PacBaseDir $ testDir </> "init" </> "Wang"]
         , _genoConvertOutFormat = "EIGENSTRAT"
-        , _genoConvertOutOnlyGeno = False
         , _genoMaybeOutPackagePath = Nothing
         , _genoconvertRemoveOld = False
         , _genoconvertOutPlinkPopMode = PlinkPopNameAsFamily
@@ -479,7 +476,6 @@ testPipelineGenoconvert testDir checkFilePath = do
               }
           ]
         , _genoConvertOutFormat = "PLINK"
-        , _genoConvertOutOnlyGeno = True
         , _genoMaybeOutPackagePath = Nothing
         , _genoconvertRemoveOld = False
         , _genoconvertOutPlinkPopMode = PlinkPopNameAsFamily
@@ -504,7 +500,6 @@ testPipelineGenoconvert testDir checkFilePath = do
               }
           ]
         , _genoConvertOutFormat = "PLINK"
-        , _genoConvertOutOnlyGeno = True
         , _genoMaybeOutPackagePath = Nothing
         , _genoconvertRemoveOld = False
         , _genoconvertOutPlinkPopMode = PlinkPopNameAsFamily
@@ -521,7 +516,6 @@ testPipelineGenoconvert testDir checkFilePath = do
     let genoconvertOpts6zipping = GenoconvertOptions {
           _genoconvertGenoSources = [PacBaseDir $ testPacsDir </> "Schiffels_2016"]
         , _genoConvertOutFormat = "PLINK"
-        , _genoConvertOutOnlyGeno = False
         , _genoMaybeOutPackagePath = Just $ testDir </> "genoconvert" </> "zip_roundtrip"
         , _genoconvertRemoveOld = False
         , _genoconvertOutPlinkPopMode = PlinkPopNameAsFamily
@@ -537,14 +531,13 @@ testPipelineGenoconvert testDir checkFilePath = do
                                         (testDir </> "genoconvert" </> "zip_roundtrip" </> "Schiffels_2016.fam") Nothing
               in  [GenoDirect $ GenotypeDataSpec gSpec Nothing]
         , _genoConvertOutFormat = "PLINK"
-        , _genoConvertOutOnlyGeno = False
         , _genoMaybeOutPackagePath = Nothing
         , _genoconvertRemoveOld = True
         , _genoconvertOutPlinkPopMode = PlinkPopNameAsFamily
         , _genoconvertOnlyLatest = False
         , _genoconvertOutZip     = False
     }
-    testLog $ runGenoconvert genoconvertOpts6unzipping
+    return ()
 
     runAndChecksumFiles checkFilePath testDir (testLog $ runGenoconvert genoconvertOpts6unzipping) "genoconvert" [
           "genoconvert" </> "zip_roundtrip" </> "Schiffels_2016.bed"