From 3e379f039c8eaffd32df66732be04bee1f8c9ed3 Mon Sep 17 00:00:00 2001
From: Derek <derekwbarnett@gmail.com>
Date: Mon, 30 Aug 2010 15:57:55 -0400
Subject: [PATCH] Fixed: Calls to GetEndPosition() rely on CIGAR data being
 parsed. Previously this was not set if BamAlignment was retrieved via
 GetNextAlignmentCore().  Moved CIGAR parsing back to LoadNextAlignment() to
 ensure this works properly.

---
 src/api/BamReader.cpp | 62 ++++++++++++++++++++++++++++---------------
 1 file changed, 41 insertions(+), 21 deletions(-)

diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp
index b1b1b5d..10aaa5e 100644
--- a/src/api/BamReader.cpp
+++ b/src/api/BamReader.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 15 July 2010 (DB)
+// Last modified: 30 August 2010 (DB)
 // ---------------------------------------------------------------------------
 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
 // Institute.
@@ -196,7 +196,7 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
   
     // calculate character lengths/offsets
     const unsigned int dataLength      = bAlignment.SupportData.BlockLength - BAM_CORE_SIZE;
-    const unsigned int cigarDataOffset = bAlignment.SupportData.QueryNameLength;
+//     const unsigned int cigarDataOffset = bAlignment.SupportData.QueryNameLength;
     const unsigned int seqDataOffset   = bAlignment.SupportData.QueryNameLength + (bAlignment.SupportData.NumCigarOperations * 4);
     const unsigned int qualDataOffset  = seqDataOffset + (bAlignment.SupportData.QuerySequenceLength+1)/2;
     const unsigned int tagDataOffset   = qualDataOffset + bAlignment.SupportData.QuerySequenceLength;
@@ -204,31 +204,30 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
       
     // set up char buffers
     const char*     allCharData = bAlignment.SupportData.AllCharData.data();
-          uint32_t* cigarData   = (uint32_t*)(allCharData + cigarDataOffset);
+//           uint32_t* cigarData   = (uint32_t*)(allCharData + cigarDataOffset);
     const char*     seqData     = ((const char*)allCharData) + seqDataOffset;
     const char*     qualData    = ((const char*)allCharData) + qualDataOffset;
           char*     tagData     = ((char*)allCharData) + tagDataOffset;
   
-    // store alignment name (depends on null char as terminator)
+    // store alignment name (relies on null char in name as terminator)
     bAlignment.Name.assign((const char*)(allCharData));    
           
-    // save CigarOps 
-    CigarOp op;
-    bAlignment.CigarData.clear();
-    bAlignment.CigarData.reserve(bAlignment.SupportData.NumCigarOperations);
-    for (unsigned int i = 0; i < bAlignment.SupportData.NumCigarOperations; ++i) {
-
-        // swap if necessary
-        if ( IsBigEndian ) { SwapEndian_32(cigarData[i]); }
-      
-        // build CigarOp structure
-        op.Length = (cigarData[i] >> BAM_CIGAR_SHIFT);
-        op.Type   = CIGAR_LOOKUP[ (cigarData[i] & BAM_CIGAR_MASK) ];
-
-        // save CigarOp
-        bAlignment.CigarData.push_back(op);
-    }
-          
+//     // save CigarOps 
+//     CigarOp op;
+//     bAlignment.CigarData.clear();
+//     bAlignment.CigarData.reserve(bAlignment.SupportData.NumCigarOperations);
+//     for (unsigned int i = 0; i < bAlignment.SupportData.NumCigarOperations; ++i) {
+// 
+//         // swap if necessary
+//         if ( IsBigEndian ) { SwapEndian_32(cigarData[i]); }
+//       
+//         // build CigarOp structure
+//         op.Length = (cigarData[i] >> BAM_CIGAR_SHIFT);
+//         op.Type   = CIGAR_LOOKUP[ (cigarData[i] & BAM_CIGAR_MASK) ];
+// 
+//         // save CigarOp
+//         bAlignment.CigarData.push_back(op);
+//     }
           
     // save query sequence
     bAlignment.QueryBases.clear();
@@ -663,6 +662,27 @@ bool BamReader::BamReaderPrivate::LoadNextAlignment(BamAlignment& bAlignment) {
         
         // set success flag
         readCharDataOK = true;
+        
+        // save CIGAR ops 
+        // need to calculate this here so that  BamAlignment::GetEndPosition() performs correctly, 
+        // even when BamReader::GetNextAlignmentCore() is called 
+        const unsigned int cigarDataOffset = bAlignment.SupportData.QueryNameLength;
+        uint32_t* cigarData = (uint32_t*)(allCharData + cigarDataOffset);
+        CigarOp op;
+        bAlignment.CigarData.clear();
+        bAlignment.CigarData.reserve(bAlignment.SupportData.NumCigarOperations);
+        for (unsigned int i = 0; i < bAlignment.SupportData.NumCigarOperations; ++i) {
+
+            // swap if necessary
+            if ( IsBigEndian ) SwapEndian_32(cigarData[i]);
+          
+            // build CigarOp structure
+            op.Length = (cigarData[i] >> BAM_CIGAR_SHIFT);
+            op.Type   = CIGAR_LOOKUP[ (cigarData[i] & BAM_CIGAR_MASK) ];
+
+            // save CigarOp
+            bAlignment.CigarData.push_back(op);
+        }
     }
 
     free(allCharData);
-- 
2.39.2