Fixed: error in BamWriter metadata output on big-endian systems

diff --git a/src/api/internal/bam/BamWriter_p.cpp b/src/api/internal/bam/BamWriter_p.cpp
index ba4989f48b7b47321e178f7c4a271928ee9b8d22..97a9a12d4b98b7ffaa1bf06a51ed0d568dd381b1 100644 (file)
--- a/src/api/internal/bam/BamWriter_p.cpp
+++ b/src/api/internal/bam/BamWriter_p.cpp
@@ -2,7 +2,7 @@
 // BamWriter_p.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
 // BamWriter_p.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------

-// Last modified: 25 October 2011 (DB)
+// Last modified: 13 February 2012 (DB)

 // ---------------------------------------------------------------------------
 // Provides the basic functionality for producing BAM files
 // ***************************************************************************
 // ---------------------------------------------------------------------------
 // Provides the basic functionality for producing BAM files
 // ***************************************************************************


@@ -283,7 +283,7 @@ void BamWriterPrivate::WriteAlignment(const BamAlignment& al) {
         pBaseQualities[i] -= 33; // FASTQ conversion
     m_stream.Write(pBaseQualities, queryLength);
 
         pBaseQualities[i] -= 33; // FASTQ conversion
     m_stream.Write(pBaseQualities, queryLength);
 

-    // write the read group tag
+    // write the tag data

     if ( m_isBigEndian ) {
 
         char* tagData = new char[tagDataLength]();
     if ( m_isBigEndian ) {
 
         char* tagData = new char[tagDataLength]();


@@ -434,13 +434,14 @@ void BamWriterPrivate::WriteReferences(const BamTools::RefVector& referenceSeque
     RefVector::const_iterator rsEnd  = referenceSequences.end();
     for ( ; rsIter != rsEnd; ++rsIter ) {
 
     RefVector::const_iterator rsEnd  = referenceSequences.end();
     for ( ; rsIter != rsEnd; ++rsIter ) {
 

-        // write the reference sequence name length
-        uint32_t referenceSequenceNameLen = rsIter->RefName.size() + 1;
-        if ( m_isBigEndian ) BamTools::SwapEndian_32(referenceSequenceNameLen);
-        m_stream.Write((char*)&referenceSequenceNameLen, Constants::BAM_SIZEOF_INT);
+        // write the reference sequence name length (+1 for terminator)
+        const uint32_t actualNameLen = rsIter->RefName.size() + 1;
+        uint32_t maybeSwappedNameLen = actualNameLen;
+        if ( m_isBigEndian ) BamTools::SwapEndian_32(maybeSwappedNameLen);
+        m_stream.Write((char*)&maybeSwappedNameLen, Constants::BAM_SIZEOF_INT);

 
         // write the reference sequence name
 
         // write the reference sequence name

-        m_stream.Write(rsIter->RefName.c_str(), referenceSequenceNameLen);
+        m_stream.Write(rsIter->RefName.c_str(), actualNameLen);

 
         // write the reference sequence length
         int32_t referenceLength = rsIter->RefLength;
 
         // write the reference sequence length
         int32_t referenceLength = rsIter->RefLength;


@@ -452,11 +453,12 @@ void BamWriterPrivate::WriteReferences(const BamTools::RefVector& referenceSeque
 void BamWriterPrivate::WriteSamHeaderText(const std::string& samHeaderText) {
 
     // write the SAM header  text length
 void BamWriterPrivate::WriteSamHeaderText(const std::string& samHeaderText) {
 
     // write the SAM header  text length

-    uint32_t samHeaderLen = samHeaderText.size();
-    if ( m_isBigEndian ) BamTools::SwapEndian_32(samHeaderLen);
-    m_stream.Write((char*)&samHeaderLen, Constants::BAM_SIZEOF_INT);
+    const uint32_t actualHeaderLen = samHeaderText.size();
+    uint32_t maybeSwappedHeaderLen = samHeaderText.size();
+    if ( m_isBigEndian ) BamTools::SwapEndian_32(maybeSwappedHeaderLen);
+    m_stream.Write((char*)&maybeSwappedHeaderLen, Constants::BAM_SIZEOF_INT);

 
     // write the SAM header text
 
     // write the SAM header text

-    if ( samHeaderLen > 0 )
-        m_stream.Write(samHeaderText.data(), samHeaderLen);
+    if ( actualHeaderLen > 0 )
+        m_stream.Write(samHeaderText.data(), actualHeaderLen);

 }
 }