From 9712fed7a53267d5916e03ccd3f27d849fbbcb25 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 27 Feb 2012 13:34:44 -0500
Subject: [PATCH] Trap SAMFormatException and rethrow as MalformatedBAM
 exception

-- Trap errors in header and rethrow
-- Wrap underlying iterator in MalformatedBAMErrorReformattingIterator
---
 .../gatk/datasources/reads/SAMDataSource.java |  3 ++
 .../MalformedBAMErrorReformatingIterator.java | 45 +++++++++++++++++++
 2 files changed, 48 insertions(+)
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java

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 bba5c21e2..b215763b5 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
@@ -570,6 +570,7 @@ public class SAMDataSource {
                 inputStream.submitAccessPlan(new SAMReaderPosition(id,inputStream,(GATKBAMFileSpan)shard.getFileSpans().get(id)));
             }
             iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id));
+            iterator = new MalformedBAMErrorReformatingIterator(id.samFile, iterator);
             if(shard.getGenomeLocs().size() > 0)
                 iterator = new IntervalOverlapFilteringIterator(iterator,shard.getGenomeLocs());
             mergingIterator.addIterator(readers.getReader(id),iterator);
@@ -873,6 +874,8 @@ public class SAMDataSource {
                     throw new UserException.CouldNotReadInputFile(readerID.samFile, e);
                 else
                     throw e;
+            } catch ( SAMFormatException e ) {
+                throw new UserException.MalformedBAM(readerID.samFile, e.getMessage());
             }
             reader.setSAMRecordFactory(factory);
             reader.enableFileSource(true);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java
new file mode 100644
index 000000000..f5dee4961
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java
@@ -0,0 +1,45 @@
+package org.broadinstitute.sting.gatk.iterators;
+
+import net.sf.samtools.SAMFormatException;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.util.CloseableIterator;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
+import java.io.File;
+import java.util.Iterator;
+
+/**
+ * Traps BAM formatting errors in underlying iterator and rethrows meaningful GATK UserExceptions
+ */
+public class MalformedBAMErrorReformatingIterator implements CloseableIterator<SAMRecord> {
+    File source;
+    CloseableIterator<SAMRecord> it;
+
+    public MalformedBAMErrorReformatingIterator(final File source, final CloseableIterator<SAMRecord> it) {
+        this.it = it;
+        this.source = source;
+    }
+
+    public boolean hasNext() {
+        try {
+            return this.it.hasNext();
+        } catch ( SAMFormatException e ) {
+            throw new UserException.MalformedBAM(source, e.getMessage());
+        }
+    }
+
+    public SAMRecord next() {
+        try {
+            return it.next();
+        } catch ( SAMFormatException e ) {
+            throw new UserException.MalformedBAM(source, e.getMessage());
+        }
+    }
+
+    public void remove() {
+        throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
+    }
+
+    public void close() { it.close(); }
+    public Iterator<SAMRecord> iterator() { return this; }
+}