fixed remove duplicates

ddcap · May 31, 2016 · ab61b3d · ab61b3d
1 parent 22f55d2
commit ab61b3d
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/halvade/src/be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.java b/halvade/src/be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.java
@@ -189,15 +189,14 @@ protected void PicardPreprocess(Context context, PreprocessingTools tools, SAMRe
         context.getCounter(HalvadeCounters.TIME_HADOOP_SAMTOBAM).increment(estimatedTime);
         Logger.DEBUG("time writing " + count + " records to disk: " + estimatedTime / 1000);
 
-        int markdup_threshold = 1000000;
 //        if (reads > markdup_threshold) {
 //            Logger.DEBUG("sample sam");
 //            context.setStatus("sample sam");
 //            tools.sampleSam(tmpOut1, tmpOut2, (double)markdup_threshold / reads);
 //        }
         Logger.DEBUG("mark duplicates");
         context.setStatus("mark duplicates");
-        tools.runMarkDuplicates(tmpOut1, gff != null ? tmpOut3 : output, tmpMetrics, keepDups && reads < markdup_threshold);
+        tools.runMarkDuplicates(tmpOut1, gff != null ? tmpOut3 : output, tmpMetrics, keepDups);
 
         if (gff != null) {
             // tmpOut3 is sam for htseq count!