From 9dc8d491959121a87f4605538394a50f3ed661c1 Mon Sep 17 00:00:00 2001 From: michael-weinstein Date: Fri, 17 Jan 2020 02:39:10 -0800 Subject: [PATCH] Final commits to make version 1.0.0 because we have our first working version. --- analyzeStandardReads.py | 2 +- reference/zrGutStandard.json | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/analyzeStandardReads.py b/analyzeStandardReads.py index 5241760..b5ec274 100644 --- 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 index dcf145d..1d15887 100644 --- 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" ]