Modified handling of BamAlignmentSupportData. This fix should allow BamWriter::SaveA...

[bamtools.git] / BamAux.h

diff --git a/BamAux.h b/BamAux.h
index c079e1dacf4d20975428be3daee638934114d5e7..f742aebb86d3f3fc88bc408757686574e5788fa4 100644 (file)
--- a/BamAux.h
+++ b/BamAux.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College\r
 // All rights reserved.\r
 // ---------------------------------------------------------------------------\r
-// Last modified: 16 June 2010 (DB)\r
+// Last modified: 15 July 2010 (DB)\r
 // ---------------------------------------------------------------------------\r
 // Provides the basic constants, data structures, etc. for using BAM files\r
 // ***************************************************************************\r
@@ -133,7 +133,8 @@ struct BamAlignment {
         int32_t      MateRefID;         // ID number for reference sequence where alignment's mate was aligned\r
         int32_t      MatePosition;      // Position (0-based) where alignment's mate starts\r
         int32_t      InsertSize;        // Mate-pair insert size\r
-        \r
+          \r
+          \r
         struct BamAlignmentSupportData {\r
       \r
             // data members\r
@@ -142,7 +143,7 @@ struct BamAlignment {
             uint32_t    NumCigarOperations;\r
             uint32_t    QueryNameLength;\r
             uint32_t    QuerySequenceLength;\r
-            bool        IsParsed;\r
+            bool        HasCoreOnly;\r
             \r
             // constructor\r
             BamAlignmentSupportData(void)\r
@@ -150,7 +151,7 @@ struct BamAlignment {
                 , NumCigarOperations(0)\r
                 , QueryNameLength(0)\r
                 , QuerySequenceLength(0)\r
-                , IsParsed(false)\r
+                , HasCoreOnly(false)\r
             { }\r
         };\r
         \r
@@ -228,46 +229,6 @@ struct BamRegion {
     { }\r
 };\r
 \r
-// ----------------------------------------------------------------\r
-// Indexing structs & typedefs\r
-\r
-struct Chunk {\r
-\r
-    // data members\r
-    uint64_t Start;\r
-    uint64_t Stop;\r
-\r
-    // constructor\r
-    Chunk(const uint64_t& start = 0, \r
-          const uint64_t& stop = 0)\r
-        : Start(start)\r
-        , Stop(stop)\r
-    { }\r
-};\r
-\r
-inline\r
-bool ChunkLessThan(const Chunk& lhs, const Chunk& rhs) {\r
-    return lhs.Start < rhs.Start;\r
-}\r
-\r
-typedef std::vector<Chunk> ChunkVector;\r
-typedef std::map<uint32_t, ChunkVector> BamBinMap;\r
-typedef std::vector<uint64_t> LinearOffsetVector;\r
-\r
-struct ReferenceIndex {\r
-    // data members\r
-    BamBinMap Bins;\r
-    LinearOffsetVector Offsets;\r
-    // constructor\r
-    ReferenceIndex(const BamBinMap& binMap = BamBinMap(),\r
-                   const LinearOffsetVector& offsets = LinearOffsetVector())\r
-        : Bins(binMap)\r
-        , Offsets(offsets)\r
-    { }\r
-};\r
-\r
-typedef std::vector<ReferenceIndex> BamIndex;\r
-\r
 // ----------------------------------------------------------------\r
 // BamAlignment member methods\r
 \r