refine QC output folders and file names

#11

preprocesser.py

@@ -304,9 +304,7 @@ def run(self):
             qc_base_folder =  os.path.join(os.path.dirname(os.path.dirname(good_dir+"/")), "QC")
         if not os.path.exists(qc_base_folder):
             os.makedirs(qc_base_folder)
-        qc_dir =  os.path.join(qc_base_folder, os.path.basename(self.options.read1_file))
-        if not os.path.exists(qc_dir):
-            os.makedirs(qc_dir)
+        qc_dir = qc_base_folder
 
         if not os.path.exists(good_dir):
             os.makedirs(good_dir)
@@ -711,15 +709,15 @@ def run(self):
             reporter.addFigure('Overlap length distribution', self.r1qc_prefilter.overlapPlotly(overlap_histgram, readLen, TOTAL_READS, 'overlap_stat'), 'overlap_stat', "")
             #self.r1qc_prefilter.plotOverlapHistgram(overlap_histgram, readLen, TOTAL_READS, os.path.join(qc_dir, "overlap.png"))
 
-        stat_file = open(os.path.join(qc_dir, "report.json"), "w")
+        stat_file = open(os.path.join(qc_dir, os.path.basename(self.options.read1_file) + ".json"), "w")
         stat_json = json.dumps(stat, sort_keys=True,indent=4, separators=(',', ': '))
         stat_file.write(stat_json)
         stat_file.close()
 
         self.addFiguresToReport(reporter)
         reporter.setStat(stat)
         reporter.setVersion(self.options.version)
-        reporter.output(os.path.join(qc_dir, "report.html"))
+        reporter.output(os.path.join(qc_dir, os.path.basename(self.options.read1_file) + ".html"))
 
     def addFiguresToReport(self, reporter):
         if self.options.read2_file != None: