Bug fix for split sam validation

njdbickhart · Jun 1, 2015 · 17f8512 · 17f8512
1 parent 8cf4214
commit 17f8512
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Showing 4 changed files with 10 additions and 5 deletions.
diff --git a/src/workers/BufferedSetReader.java b/src/workers/BufferedSetReader.java
@@ -244,6 +244,7 @@ private SetMap<BufferedInitialSet> associateSplits(HashMap<String, ArrayList<anc
         this.hardUnbal = 0;
 
         try(SAMFileReader samReader = new SAMFileReader(file.getSplitsam().toFile())){
+            samReader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
             SAMRecordIterator iterator = samReader.iterator();
             while(iterator.hasNext()){
                 SAMRecord line = iterator.next();

diff --git a/src/workers/OutputEvents.java b/src/workers/OutputEvents.java
@@ -27,6 +27,8 @@ public class OutputEvents {
     protected Path supportfile;
     protected final boolean debug;
 
+    private static final Logger log = Logger.getLogger(OutputEvents.class.getName());
+
     public OutputEvents(String outfile, boolean debug){
         //this.sets = (ArrayList<finalSets>) sets;
         this.outfile = Paths.get(outfile);
@@ -37,14 +39,16 @@ public OutputEvents(String outfile, boolean debug){
             try {
                 this.outfile.toFile().createNewFile();
             } catch (IOException ex) {
-                Logger.getLogger(OutputEvents.class.getName()).log(Level.SEVERE, null, ex);
+                log.log(Level.SEVERE, "[OUTPUTEVENTS] Could not create new output file: " + outfile, ex);
+                System.exit(-1);
             }
         else{
             this.outfile.toFile().delete();
             try {
                 this.outfile.toFile().createNewFile();
             } catch (IOException ex) {
-                Logger.getLogger(OutputEvents.class.getName()).log(Level.SEVERE, null, ex);
+                log.log(Level.SEVERE, "[OUTPUTEVENTS] Could not overwrite existing output file: " + outfile, ex);
+                System.exit(-1);
             }
         }
     }
@@ -72,7 +76,7 @@ public void WriteOut (){
                 //output.newLine();
             }
         } catch (IOException ex) {
-            Logger.getLogger(OutputEvents.class.getName()).log(Level.SEVERE, null, ex);
+            log.log(Level.SEVERE, "[OUTPUTEVENTS] Could not write to outfile: " + this.outfile.toString(), ex);
         }
 
         if(debug){
@@ -83,7 +87,7 @@ public void WriteOut (){
                     support.newLine();
                 }
             }catch(IOException ex){
-                Logger.getLogger(OutputEvents.class.getName()).log(Level.SEVERE, null, ex);
+                log.log(Level.SEVERE, "[OUTPUTEVENTS] Could not write to supportfile: " + this.supportfile.toString(), ex);
             }
         }
     }

diff --git a/src/workers/RPSRmain.java b/src/workers/RPSRmain.java
@@ -24,7 +24,7 @@
  * @author bickhart
  */
 public class RPSRmain {
-    private static final String version = "0.0.13";
+    private static final String version = "0.0.14";
     private static final Logger log = Logger.getLogger(RPSRmain.class.getName());
     /**
      * @param args the command line arguments

diff --git a/store/RAPTR-SV.jar b/store/RAPTR-SV.jar