Final commits to make version 1.0.0 because we have our first working…

… version.
Zymo-Research · Jan 17, 2020 · 9dc8d49 · 9dc8d49
1 parent db9ef98
commit 9dc8d49
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/analyzeStandardReads.py b/analyzeStandardReads.py
@@ -249,7 +249,7 @@ def generateReport(result:miqScoreNGSReadCountPublic.MiqScoreData):
     logger.debug("Starting analysis")
     bamFilePath = os.path.join(parameters.outputFolder.value, "%s.bam" %parameters.sampleName.value)
     if applicationMode == "PE":
-        #miqScoreShotgunPublicSupport.alignmentAnalysis.bwaHandler.bwaAlignPE(parameters.forwardReads.value, parameters.reverseReads.value, parameters.workingFolder.value, bamFilePath, parameters.referenceGenome.value) #TODO Return this line to functionality if disabled
+        miqScoreShotgunPublicSupport.alignmentAnalysis.bwaHandler.bwaAlignPE(parameters.forwardReads.value, parameters.reverseReads.value, parameters.workingFolder.value, bamFilePath, parameters.referenceGenome.value)
         readTable = miqScoreShotgunPublicSupport.alignmentAnalysis.alignmentAnalysisPE.bamFileProcessor(bamFilePath)
     elif applicationMode == "SE":
         miqScoreShotgunPublicSupport.alignmentAnalysis.bwaHandler.bwaAlignSE(parameters.reads.value, parameters.workingFolder.value, bamFilePath, parameters.referenceGenome.value)

diff --git a/reference/zrGutStandard.json b/reference/zrGutStandard.json
@@ -88,14 +88,14 @@
                 "calbican",
                 "scerevisiae",
                 "rhominis",
+                "badolescentis",
+                "lfermentum",
                 "cdifficille",
                 "fprausnitzii",
-                "lfermentum",
-                "badolescentis",
+                "amuciniphila",
                 "fnucleatum",
                 "vrogosae",
                 "pcorporis",
-                "amuciniphila",
                 "bfragilis",
                 "ecoli"
             ]