Major speedup in SamSequenceDictionary & SamReadGroupDictionary classes

[bamtools.git] / src / api / internal / SamHeaderValidator_p.cpp

diff --git a/src/api/internal/SamHeaderValidator_p.cpp b/src/api/internal/SamHeaderValidator_p.cpp
index 75e2c135ff9f35ff1d929b800691af64d8dedb1c..9d7f6d42dcb6c63fba649827edb2a71cf581583a 100644 (file)
--- a/src/api/internal/SamHeaderValidator_p.cpp
+++ b/src/api/internal/SamHeaderValidator_p.cpp
@@ -2,15 +2,15 @@
 // SamHeaderValidator.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 6 October 2011 (DB)
+// Last modified: 12 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides functionality for validating SamHeader data
 // ***************************************************************************
 
-#include <api/SamConstants.h>
-#include <api/SamHeader.h>
-#include <api/internal/SamHeaderValidator_p.h>
-#include <api/internal/SamHeaderVersion_p.h>
+#include "api/SamConstants.h"
+#include "api/SamHeader.h"
+#include "api/internal/SamHeaderValidator_p.h"
+#include "api/internal/SamHeaderVersion_p.h"
 using namespace BamTools;
 using namespace BamTools::Internal;
 
@@ -244,7 +244,7 @@ bool SamHeaderValidator::ValidateSequenceDictionary(void) {
     SamSequenceConstIterator seqIter = sequences.ConstBegin();
     SamSequenceConstIterator seqEnd  = sequences.ConstEnd();
     for ( ; seqIter != seqEnd; ++seqIter ) {
-        const SamSequence& seq = (*seqIter);
+        const SamSequence& seq = seqIter->second;
         isValid &= ValidateSequence(seq);
     }
 
@@ -264,7 +264,7 @@ bool SamHeaderValidator::ContainsUniqueSequenceNames(void) {
     SamSequenceConstIterator seqIter = sequences.ConstBegin();
     SamSequenceConstIterator seqEnd  = sequences.ConstEnd();
     for ( ; seqIter != seqEnd; ++seqIter ) {
-        const SamSequence& seq = (*seqIter);
+        const SamSequence& seq = seqIter->second;
 
         // lookup sequence name
         const string& name = seq.Name;
@@ -348,7 +348,7 @@ bool SamHeaderValidator::ValidateReadGroupDictionary(void) {
     SamReadGroupConstIterator rgIter = readGroups.ConstBegin();
     SamReadGroupConstIterator rgEnd  = readGroups.ConstEnd();
     for ( ; rgIter != rgEnd; ++rgIter ) {
-        const SamReadGroup& rg = (*rgIter);
+        const SamReadGroup& rg = rgIter->second;
         isValid &= ValidateReadGroup(rg);
     }
 
@@ -370,7 +370,7 @@ bool SamHeaderValidator::ContainsUniqueIDsAndPlatformUnits(void) {
     SamReadGroupConstIterator rgIter = readGroups.ConstBegin();
     SamReadGroupConstIterator rgEnd  = readGroups.ConstEnd();
     for ( ; rgIter != rgEnd; ++rgIter ) {
-        const SamReadGroup& rg = (*rgIter);
+        const SamReadGroup& rg = rgIter->second;
 
         // --------------------------------
         // check for unique ID