Fixed lineage_wf CLI bug causing crash due to missing coverage_file a…

…rgument
Ecogenomics · Jan 3, 2018 · 8902888 · 8902888
1 parent ee3a41d
commit 8902888
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Showing 2 changed files with 13 additions and 2 deletions.
diff --git a/checkm/VERSION b/checkm/VERSION
@@ -1,3 +1,5 @@
+1.0.11
+- fix to lineage_wf CLI regarding missing coverage_file argument
 1.0.10
 - updated version number for pypi
 1.0.9

diff --git a/checkm/main.py b/checkm/main.py
@@ -413,8 +413,16 @@ def qa(self, options):
                           )
 
         self.logger.info('')
-        RP.printSummary(options.out_format, aai, binIdToBinMarkerSets, options.bIndividualMarkers, options.coverage_file, options.bTabTable, options.file, anaFolder=options.analyze_folder)
-        RP.cacheResults(options.analyze_folder, binIdToBinMarkerSets, options.bIndividualMarkers)
+        RP.printSummary(options.out_format, 
+                        aai, binIdToBinMarkerSets, 
+                        options.bIndividualMarkers, 
+                        options.coverage_file, 
+                        options.bTabTable, 
+                        options.file, 
+                        anaFolder=options.analyze_folder)
+        RP.cacheResults(options.analyze_folder, 
+                            binIdToBinMarkerSets, 
+                            options.bIndividualMarkers)
 
         if options.file != '':
             self.logger.info('  QA information written to: ' + options.file)
@@ -1240,6 +1248,7 @@ def parseOptions(self, options):
             options.out_format = 1
             options.bAlignTopHit = False
             options.exclude_markers = None
+            options.coverage_file = None
 
             self.tree(options)
             self.lineageSet(options)