clean up commented code and update file extensions

vgteam · Aug 20, 2024 · f4fd676 · f4fd676
1 parent 01d1c8e
commit f4fd676
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Showing 3 changed files with 2 additions and 5 deletions.
diff --git a/docker/config.json b/docker/config.json
@@ -84,7 +84,7 @@
   "fileTypeToExtensions": {
     "graph": ".xg,.vg,.hg,.gbz,.pg,.db",
     "haplotype": ".gbwt,.gbz",
-    "read": ".gam"
+    "read": ".gam,gaf.gz"
   },
 
   "MAXUPLOADSIZE": 5242880,

diff --git a/src/config.json b/src/config.json
@@ -114,7 +114,7 @@
   "fileTypeToExtensions": {
     "graph": ".xg,.vg,.hg,.gbz,.pg,.db",
     "haplotype": ".gbwt,.gbz",
-    "read": ".gam"
+    "read": ".gam,.gaf.gz"
   },
 
   "MAXUPLOADSIZE": 5242880,

diff --git a/src/server.mjs b/src/server.mjs
@@ -1206,9 +1206,6 @@ function processGamFile(req, res, next, gamFile, gamFileNumber) {
       vgViewParams.push("-");
       // vg convert needs the graph to convert GAF to GAM
       const graphFile = getFirstFileOfType(req.body.tracks, fileTypes.GRAPH);
-      // let dataPath = pickDataPath(req.body.dataPath);
-      // console.log(`dataPath = ${dataPath}`);
-      // vgConvertParams.push("-F", gamFile, `${dataPath}${graphFile}`);
       vgConvertParams.push("-F", gamFile, graphFile);
     }
     if (gamFile.endsWith(".gam")) {