Fixed: regression in convert tool - SAM tags contained unreadable chars for int8...

[bamtools.git] / src / toolkit / bamtools_convert.cpp

diff --git a/src/toolkit/bamtools_convert.cpp b/src/toolkit/bamtools_convert.cpp
index f3bc486d85df74f7abb956e7d65ce8b03c801a85..0e1743ffcba56a1859fbe946c3a345f890ac037a 100644 (file)
--- a/src/toolkit/bamtools_convert.cpp
+++ b/src/toolkit/bamtools_convert.cpp
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // bamtools_convert.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 11 June 2011
+// Last modified: 11 November 2012
 // ---------------------------------------------------------------------------
 // Converts between BAM and a number of other formats
 // ***************************************************************************
@@ -278,7 +277,7 @@ void ConvertTool::ConvertToolPrivate::PrintBed(const BamAlignment& a) {
 
     m_out << m_references.at(a.RefID).RefName << "\t"
           << a.Position << "\t"
-          << a.GetEndPosition() + 1 << "\t"
+          << a.GetEndPosition() << "\t"
           << a.Name << "\t"
           << a.MapQuality << "\t"
           << (a.IsReverseStrand() ? "-" : "+") << endl;
@@ -397,7 +396,7 @@ void ConvertTool::ConvertToolPrivate::PrintJson(const BamAlignment& a) {
         m_out << "\"queryBases\":\"" << a.QueryBases << "\",";
     
     // write qualities
-    if ( !a.Qualities.empty() ) {
+    if ( !a.Qualities.empty() && a.Qualities.at(0) != (char)0xFF ) {
         string::const_iterator s = a.Qualities.begin();
         m_out << "\"qualities\":[" << static_cast<short>(*s) - 33;
         ++s;
@@ -435,9 +434,15 @@ void ConvertTool::ConvertToolPrivate::PrintJson(const BamAlignment& a) {
                     ++index; 
                     break;
                 
-                case (Constants::BAM_TAG_TYPE_INT8)  :
+                case (Constants::BAM_TAG_TYPE_INT8) :
+                    // force value into integer-type (instead of char value)
+                    m_out << static_cast<int16_t>(tagData[index]);
+                    ++index;
+                    break;
+
                 case (Constants::BAM_TAG_TYPE_UINT8) :
-                    m_out << (int)tagData[index]; 
+                    // force value into integer-type (instead of char value)
+                    m_out << static_cast<uint16_t>(tagData[index]);
                     ++index; 
                     break;
                 
@@ -498,8 +503,8 @@ void ConvertTool::ConvertToolPrivate::PrintSam(const BamAlignment& a) {
     // <QNAME> <FLAG> <RNAME> <POS> <MAPQ> <CIGAR> <MRNM> <MPOS> <ISIZE> <SEQ> <QUAL> [ <TAG>:<VTYPE>:<VALUE> [...] ]
   
     // write name & alignment flag
-    m_out << a.Name << "\t" << a.AlignmentFlag << "\t";
-    
+   m_out << a.Name << "\t" << a.AlignmentFlag << "\t";
+
     // write reference name
     if ( (a.RefID >= 0) && (a.RefID < (int)m_references.size()) ) 
         m_out << m_references[a.RefID].RefName << "\t";
@@ -527,7 +532,7 @@ void ConvertTool::ConvertToolPrivate::PrintSam(const BamAlignment& a) {
         if ( a.MateRefID == a.RefID )
             m_out << "=\t";
         else
-            m_out << m_references[a.MateRefID].RefName << "\t";
+           m_out << m_references[a.MateRefID].RefName << "\t";
         m_out << a.MatePosition+1 << "\t" << a.InsertSize << "\t";
     } 
     else
@@ -540,7 +545,7 @@ void ConvertTool::ConvertToolPrivate::PrintSam(const BamAlignment& a) {
         m_out << a.QueryBases << "\t";
     
     // write qualities
-    if ( a.Qualities.empty() )
+    if ( a.Qualities.empty() || (a.Qualities.at(0) == (char)0xFF) )
         m_out << "*";
     else
         m_out << a.Qualities;
@@ -566,9 +571,15 @@ void ConvertTool::ConvertToolPrivate::PrintSam(const BamAlignment& a) {
                 ++index;
                 break;
 
-            case (Constants::BAM_TAG_TYPE_INT8)  :
+            case (Constants::BAM_TAG_TYPE_INT8) :
+                // force value into integer-type (instead of char value)
+                m_out << "i:" << static_cast<int16_t>(tagData[index]);
+                ++index;
+                break;
+
             case (Constants::BAM_TAG_TYPE_UINT8) :
-                m_out << "i:" << (int)tagData[index];
+                // force value into integer-type (instead of char value)
+                m_out << "i:" << static_cast<uint16_t>(tagData[index]);
                 ++index;
                 break;
 
@@ -597,7 +608,7 @@ void ConvertTool::ConvertToolPrivate::PrintSam(const BamAlignment& a) {
                 index += sizeof(float);
                 break;
 
-            case (Constants::BAM_TAG_TYPE_HEX)    :
+            case (Constants::BAM_TAG_TYPE_HEX)    : // fall-through
             case (Constants::BAM_TAG_TYPE_STRING) :
                 m_out << type << ":";
                 while (tagData[index]) {
@@ -608,7 +619,7 @@ void ConvertTool::ConvertToolPrivate::PrintSam(const BamAlignment& a) {
                 break;
         }
 
-        if ( tagData[index] == '\0') 
+        if ( tagData[index] == '\0' )
             break;
     }