Auto adjust insert size in pindel analysis

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PindelAnalysis.java

@@ -120,7 +120,13 @@ private static String parseInsertMetrics(File inputFile) throws IOException
             {
                 if (m.PAIR_ORIENTATION == SamPairUtil.PairOrientation.FR)
                 {
-                    return String.valueOf(Math.max(100, Math.ceil(m.MEAN_INSERT_SIZE)));
+                    Double insertSize = Math.ceil(m.MEAN_INSERT_SIZE);
+                    if (insertSize < 75)
+                    {
+                        insertSize = insertSize + 150;
+                    }
+
+                    return String.valueOf(Math.max(200, insertSize.intValue()));
                 }
             }
         }