From 6885e2d065d32dfa1dc5786560b83aeed6982969 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 10 Apr 2012 07:37:42 -0400
Subject: [PATCH] UserException fixes for GATK_logs recent errors

-- SamFileReader.java:525
-- BlockCompressedInputStream:376

These were both instances were we weren't catching and rethrowing picard exceptions as UserExceptions.
---
 .../gatk/datasources/reads/SAMDataSource.java | 31 +++++++++----------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
index bf7afe4f0..bbcbe6dbc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
@@ -51,11 +51,10 @@ import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.util.*;
-import java.util.concurrent.*;
+import java.util.concurrent.Callable;
 
 /**
  * User: aaron
@@ -474,7 +473,6 @@ public class SAMDataSource {
     /**
      * Fill the given buffering shard with reads.
      * @param shard Shard to fill.
-     * @return true if at the end of the stream.  False otherwise.
      */
     public void fillShard(Shard shard) {
         if(!shard.buffersReads())
@@ -569,15 +567,19 @@ public class SAMDataSource {
             if(shard.getFileSpans().get(id) == null)
                 throw new ReviewedStingException("SAMDataSource: received null location for reader " + id + ", but null locations are no longer supported.");
 
-            if(threadAllocation.getNumIOThreads() > 0) {
-                BlockInputStream inputStream = readers.getInputStream(id);
-                inputStream.submitAccessPlan(new BAMAccessPlan(id, inputStream, (GATKBAMFileSpan) shard.getFileSpans().get(id)));
-                BAMRecordCodec codec = new BAMRecordCodec(getHeader(id),factory);
-                codec.setInputStream(inputStream);
-                iterator = new BAMCodecIterator(inputStream,readers.getReader(id),codec);
-            }
-            else {
-                iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id));
+            try {
+                if(threadAllocation.getNumIOThreads() > 0) {
+                    BlockInputStream inputStream = readers.getInputStream(id);
+                    inputStream.submitAccessPlan(new BAMAccessPlan(id, inputStream, (GATKBAMFileSpan) shard.getFileSpans().get(id)));
+                    BAMRecordCodec codec = new BAMRecordCodec(getHeader(id),factory);
+                    codec.setInputStream(inputStream);
+                    iterator = new BAMCodecIterator(inputStream,readers.getReader(id),codec);
+                }
+                else {
+                    iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id));
+                }
+            } catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFormatExceptions) sometimes
+                throw new UserException.MalformedBAM(id.samFile, e.getMessage());
             }
 
             iterator = new MalformedBAMErrorReformatingIterator(id.samFile, iterator);
@@ -932,10 +934,7 @@ public class SAMDataSource {
                     blockInputStream = new BlockInputStream(dispatcher,readerID,false);
                 reader = new SAMFileReader(readerID.samFile,indexFile,false);
             } catch ( RuntimeIOException e ) {
-                if ( e.getCause() != null && e.getCause() instanceof FileNotFoundException )
-                    throw new UserException.CouldNotReadInputFile(readerID.samFile, e);
-                else
-                    throw e;
+                throw new UserException.CouldNotReadInputFile(readerID.samFile, e);
             } catch ( SAMFormatException e ) {
                 throw new UserException.MalformedBAM(readerID.samFile, e.getMessage());
             }