Removed more non-standard STL calls from BamIndex.cpp

diff --git a/src/api/BamIndex.cpp b/src/api/BamIndex.cpp
index 5e53a117b86269e10e5a05bcb343494ef092d4d9..e72db5ff35c00c481347d6d5277b82d324e71f59 100644 (file)
--- a/src/api/BamIndex.cpp
+++ b/src/api/BamIndex.cpp
@@ -454,7 +454,9 @@ bool BamStandardIndex::BamStandardIndexPrivate::Build(void) {
         if ( (bAlignment.RefID >= 0) && (bAlignment.Bin < 4681) ) {
 
             // save linear offset entry (matched to BAM entry refID)
-            ReferenceIndex& refIndex    = m_indexData.at(bAlignment.RefID);
+           BamStandardIndexData::iterator indexIter = m_indexData.find(bAlignment.RefID);
+           if ( indexIter == m_indexData.end() ) return false; // error
+           ReferenceIndex& refIndex = (*indexIter).second;
             LinearOffsetVector& offsets = refIndex.Offsets;
             SaveLinearOffset(offsets, bAlignment, lastOffset);
         }
@@ -466,7 +468,9 @@ bool BamStandardIndex::BamStandardIndexPrivate::Build(void) {
             if ( saveBin != defaultValue ) {
 
                 // save Bam bin entry
-                ReferenceIndex& refIndex = m_indexData.at(saveRefID);
+               BamStandardIndexData::iterator indexIter = m_indexData.find(saveRefID);
+               if ( indexIter == m_indexData.end() ) return false; // error
+               ReferenceIndex& refIndex = (*indexIter).second;
                 BamBinMap& binMap = refIndex.Bins;
                 SaveBinEntry(binMap, saveBin, saveOffset, lastOffset);
             }
@@ -501,7 +505,9 @@ bool BamStandardIndex::BamStandardIndexPrivate::Build(void) {
     // save any leftover BAM data (as long as refID is valid)
     if ( saveRefID >= 0 ) {
         // save Bam bin entry
-        ReferenceIndex& refIndex = m_indexData.at(saveRefID);
+       BamStandardIndexData::iterator indexIter = m_indexData.find(saveRefID);
+       if ( indexIter == m_indexData.end() ) return false; // error
+       ReferenceIndex& refIndex = (*indexIter).second;
         BamBinMap& binMap = refIndex.Bins;
         SaveBinEntry(binMap, saveBin, saveOffset, lastOffset);
     }
@@ -558,11 +564,12 @@ void BamStandardIndex::BamStandardIndexPrivate::ClearAllData(void) {
 // clear all index offset data for desired reference
 void BamStandardIndex::BamStandardIndexPrivate::ClearReferenceOffsets(const int& refId) {
 
-    // look up desired reference, skip if not found
-    if ( m_indexData.find(refId) == m_indexData.end() ) return;
+    // look up refId, skip if not found
+    BamStandardIndexData::iterator indexIter = m_indexData.find(refId);
+    if ( indexIter == m_indexData.end() ) return ;
 
     // clear reference data
-    ReferenceIndex& refEntry = m_indexData.at(refId);
+    ReferenceIndex& refEntry = (*indexIter).second;
     refEntry.Bins.clear();
     refEntry.Offsets.clear();
 
@@ -598,7 +605,9 @@ bool BamStandardIndex::BamStandardIndexPrivate::GetOffsets(const BamRegion& regi
     int numBins = BinsFromRegion(region, isRightBoundSpecified, bins);
 
     // get bins for this reference
-    const ReferenceIndex& refIndex = m_indexData.at(region.LeftRefID);
+    BamStandardIndexData::const_iterator indexIter = m_indexData.find(region.LeftRefID);
+    if ( indexIter == m_indexData.end() ) return false; // error
+    const ReferenceIndex& refIndex = (*indexIter).second;
     const BamBinMap& binMap        = refIndex.Bins;
 
     // get minimum offset to consider
@@ -646,8 +655,9 @@ bool BamStandardIndex::BamStandardIndexPrivate::GetOffsets(const BamRegion& regi
 
 // returns whether reference has alignments or no
 bool BamStandardIndex::BamStandardIndexPrivate::HasAlignments(const int& refId) const {
-    if ( m_indexData.find(refId) == m_indexData.end()) return false;
-    const ReferenceIndex& refEntry = m_indexData.at(refId);
+    BamStandardIndexData::const_iterator indexIter = m_indexData.find(refId);
+    if ( indexIter == m_indexData.end() ) return false; // error
+    const ReferenceIndex& refEntry = (*indexIter).second;
     return refEntry.HasAlignments;
 }
 
@@ -658,9 +668,16 @@ bool BamStandardIndex::BamStandardIndexPrivate::HasFullDataCache(void) const {
 
 // returns true if index cache has data for desired reference
 bool BamStandardIndex::BamStandardIndexPrivate::IsDataLoaded(const int& refId) const {
-    if ( m_indexData.find(refId) == m_indexData.end() ) return false; // unknown reference
-    const ReferenceIndex& refEntry = m_indexData.at(refId);
-    if ( !refEntry.HasAlignments ) return true; // no data period
+
+    // look up refId, return false if not found
+    BamStandardIndexData::const_iterator indexIter = m_indexData.find(refId);
+    if ( indexIter == m_indexData.end() ) return false;
+
+    // see if reference has alignments
+    // if not, it's not a problem to have no offset data
+    const ReferenceIndex& refEntry = (*indexIter).second;
+    if ( !refEntry.HasAlignments ) return true;
+
     // return whether bin map contains data
     return ( !refEntry.Bins.empty() );
 }
@@ -909,15 +926,19 @@ bool BamStandardIndex::BamStandardIndexPrivate::LoadFirstReference(bool saveData
 // @saveData - save data in memory if true, just read & discard if false
 bool BamStandardIndex::BamStandardIndexPrivate::LoadReference(const int& refId, bool saveData) {    
 
+    // look up refId
+    BamStandardIndexData::iterator indexIter = m_indexData.find(refId);
+
     // if reference not previously loaded, create new entry
-    if ( m_indexData.find(refId) == m_indexData.end() ) {
+    if ( indexIter == m_indexData.end() ) {
         ReferenceIndex newEntry;
         newEntry.HasAlignments = false;
         m_indexData.insert( pair<int32_t, ReferenceIndex>(refId, newEntry) );
     }
 
     // load reference data
-    ReferenceIndex& entry = m_indexData.at(refId);
+    indexIter = m_indexData.find(refId);
+    ReferenceIndex& entry = (*indexIter).second;
     bool loadedOk = true;
     loadedOk &= LoadBins(entry, saveData);
     loadedOk &= LoadLinearOffsets(entry, saveData);