changed validation stringency flags

njdbickhart · Jan 29, 2015 · 7a882df · 7a882df
1 parent ff13372
commit 7a882df
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/src/modes/PreprocessMode.java b/src/modes/PreprocessMode.java
@@ -80,7 +80,7 @@ public void run(){
 
         // Run through the BAM file generating split and divet data
         final SAMFileReader reader = new SAMFileReader(new File(input));
-        reader.setValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
+        reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
 
         SAMFileHeader h = reader.getFileHeader();
         List<BedSimple> coords = this.getSamIntervals(h);
@@ -90,7 +90,7 @@ public void run(){
                 SamRecordMatcher w = new SamRecordMatcher(samplimit, checkRG, utilities.GetBaseName.getBaseName(outbase) + ".tmp", values, debug);
                 try{
                     SAMFileReader temp = new SAMFileReader(new File(input));
-                    temp.setValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
+                    temp.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
                     SAMRecordIterator itr = temp.queryContained(b.Chr(), b.Start(), b.End());
                     itr.forEachRemaining((k) -> w.bufferedAdd(k));
                     temp.close();
@@ -127,7 +127,7 @@ public void run(){
         itr.close();*/
 
         SAMFileReader next = new SAMFileReader(new File(input));
-        next.setValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
+        next.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
         worker.convertToVariant(divets, splits);
         worker.RetrieveMissingAnchors(splits, next.iterator());
 

diff --git a/src/workers/BamMetadataGeneration.java b/src/workers/BamMetadataGeneration.java
@@ -52,6 +52,7 @@ public BamMetadataGeneration(boolean hasRG){
      */
     public void ScanFile(String input, int samplimit){
         SAMFileReader sam = new SAMFileReader(new File(input));
+        sam.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
         if(!sam.hasIndex()){
             System.out.println("[METADATA] Could not find bam index file. Creating one now...");
             BAMIndexer b = new BAMIndexer(new File(input + ".bai"), sam.getFileHeader());
@@ -63,7 +64,7 @@ public void ScanFile(String input, int samplimit){
             System.out.println("[METADATA] Finished with bam index generation.");
             sam = new SAMFileReader(new File(input));
         }
-        sam.setValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
+        //sam.setValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
         header = sam.getFileHeader();
         if(expectRG){