X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamReader.cpp;h=0728d962141b559c6f8ce7d69a9721c9c02a7a52;hb=d1c8508ec5cbeafd6a1e5af4756059ccf168216f;hp=6e4a10f80ece0b7b6cfd0d55c125f6dd509bf012;hpb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;p=bamtools.git

diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp
index 6e4a10f..0728d96 100644
--- a/src/api/BamReader.cpp
+++ b/src/api/BamReader.cpp
@@ -2,13 +2,13 @@
 // BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
+// Last modified: 18 November 2012 (DB)
 // ---------------------------------------------------------------------------
 // Provides read access to BAM files.
 // ***************************************************************************
 
 #include "api/BamReader.h"
-#include "api/internal/BamReader_p.h"
+#include "api/internal/bam/BamReader_p.h"
 using namespace BamTools;
 using namespace BamTools::Internal;
 
@@ -61,6 +61,22 @@ bool BamReader::CreateIndex(const BamIndex::IndexType& type) {
     return d->CreateIndex(type);
 }
 
+/*! \fn const SamHeader& BamReader::GetConstSamHeader(void) const
+    \brief Returns const reference to SAM header data.
+
+    Allows for read-only queries of SAM header data.
+
+    If you do not need to modify the SAM header, use this method to avoid the
+    potentially expensive copy used by GetHeader().
+
+    \note
+    \returns const reference to header data object
+    \sa GetHeader(), GetHeaderText()
+*/
+const SamHeader& BamReader::GetConstSamHeader(void) const {
+    return d->GetConstSamHeader();
+}
+
 /*! \fn std::string BamReader::GetErrorString(void) const
     \brief Returns a human-readable description of the last error that occurred
 
@@ -90,7 +106,8 @@ const std::string BamReader::GetFilename(void) const {
 /*! \fn SamHeader BamReader::GetHeader(void) const
     \brief Returns SAM header data.
 
-    Header data is wrapped in a SamHeader object that can be conveniently queried & modified.
+    Header data is wrapped in a SamHeader object that can be conveniently queried and/or modified.
+    If you only need read access, consider using GetConstSamHeader() instead.
 
     \note Modifying the retrieved SamHeader object does NOT affect the
     current BAM file. This file has been opened in a read-only mode.
@@ -98,7 +115,7 @@ const std::string BamReader::GetFilename(void) const {
     BamWriter to generate a new BAM file with the appropriate header information.
 
     \returns header data object
-    \sa GetHeaderText()
+    \sa GetConstSamHeader(), GetHeaderText()
 */
 SamHeader BamReader::GetHeader(void) const {
     return d->GetSamHeader();
@@ -310,19 +327,6 @@ void BamReader::SetIndex(BamIndex* index) {
     d->SetIndex(index);
 }
 
-/*! \fn void BamReader::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode)
-    \brief Changes the caching behavior of the index data.
-
-    Default mode is BamIndex::LimitedIndexCaching.
-
-    \param[in] mode desired cache mode for index, see BamIndex::IndexCacheMode for
-                    description of the available cache modes
-    \sa HasIndex()
-*/
-void BamReader::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) {
-    d->SetIndexCacheMode(mode);
-}
-
 /*! \fn bool BamReader::SetRegion(const BamRegion& region)
     \brief Sets a target region of interest