Ensure FASTQ file groups sorted prior to merge

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/FileGroup.java

@@ -1,17 +1,15 @@
 package org.labkey.sequenceanalysis;
 
-import org.json.JSONObject;
-import org.labkey.api.util.Pair;
-
 import java.io.File;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.HashMap;
+import java.util.Comparator;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeMap;
 
 /**
  * Created by bimber on 2/19/2015.
@@ -35,7 +33,7 @@ public Set<String> getPlatformUnits()
     public List<List<FilePair>> groupByPlatformUnit()
     {
         List<List<FilePair>> ret = new ArrayList<>();
-        Map<String, List<FilePair>> grouped = new HashMap<>();
+        Map<String, List<FilePair>> grouped = new TreeMap<>();
 
         for (FilePair pair : filePairs)
         {
@@ -47,13 +45,18 @@ public List<List<FilePair>> groupByPlatformUnit()
             {
                 if (!grouped.containsKey(pair.platformUnit))
                 {
-                    grouped.put(pair.platformUnit, new ArrayList<FilePair>());
+                    grouped.put(pair.platformUnit, new ArrayList<>());
                 }
 
                 grouped.get(pair.platformUnit).add(pair);
             }
         }
 
+        for (String key : grouped.keySet())
+        {
+            grouped.get(key).sort(Comparator.comparing(filePair -> filePair.file1));
+        }
+
         ret.addAll(grouped.values());
 
         return ret;