From 19077d59154eeb244af96b1fd9658e535c24c1be Mon Sep 17 00:00:00 2001
From: derek <derekwbarnett@gmail.com>
Date: Tue, 11 Oct 2011 00:04:54 -0400
Subject: [PATCH] Removed index cache mode
---
src/api/BamIndex.h | 8 --------
src/api/BamMultiReader.cpp | 13 -------------
src/api/BamMultiReader.h | 2 --
src/api/BamReader.cpp | 13 -------------
src/api/BamReader.h | 2 --
src/api/internal/BamMultiReader_p.cpp | 16 ----------------
src/api/internal/BamMultiReader_p.h | 1 -
src/api/internal/BamRandomAccessController_p.cpp | 15 +--------------
src/api/internal/BamRandomAccessController_p.h | 2 --
src/api/internal/BamReader_p.cpp | 5 -----
src/api/internal/BamReader_p.h | 1 -
src/api/internal/BamStandardIndex_p.cpp | 7 -------
src/api/internal/BamStandardIndex_p.h | 3 ---
src/api/internal/BamToolsIndex_p.cpp | 7 -------
src/api/internal/BamToolsIndex_p.h | 3 ---
15 files changed, 1 insertion(+), 97 deletions(-)
diff --git a/src/api/BamIndex.h b/src/api/BamIndex.h
index 5e40d87..b0b1281 100644
--- a/src/api/BamIndex.h
+++ b/src/api/BamIndex.h
@@ -35,11 +35,6 @@ class API_EXPORT BamIndex {
// enums
public:
- // specify index-caching behavior
- enum IndexCacheMode { FullIndexCaching = 0 // store entire index file contents in memory
- , LimitedIndexCaching // store only index data for current reference
- , NoIndexCaching // do not store any index data between jumps
- };
// list of supported BamIndex types
enum IndexType { BAMTOOLS = 0
@@ -71,9 +66,6 @@ class API_EXPORT BamIndex {
// loads existing data from file into memory
virtual bool Load(const std::string& filename) =0;
- // change the index caching behavior
- virtual void SetCacheMode(const BamIndex::IndexCacheMode& mode) =0;
-
//! \cond
// internal methods
diff --git a/src/api/BamMultiReader.cpp b/src/api/BamMultiReader.cpp
index 6efeff6..ef38469 100644
--- a/src/api/BamMultiReader.cpp
+++ b/src/api/BamMultiReader.cpp
@@ -321,19 +321,6 @@ bool BamMultiReader::Rewind(void) {
return d->Rewind();
}
-/*! \fn void BamMultiReader::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(), BamReader::SetIndexCacheMode()
-*/
-void BamMultiReader::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) {
- d->SetIndexCacheMode(mode);
-}
-
/*! \fn bool BamMultiReader::SetRegion(const BamRegion& region)
\brief Sets a target region of interest
diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h
index 76d0810..ea068d0 100644
--- a/src/api/BamMultiReader.h
+++ b/src/api/BamMultiReader.h
@@ -97,8 +97,6 @@ class API_EXPORT BamMultiReader {
bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
// opens index files for current BAM files.
bool OpenIndexes(const std::vector<std::string>& indexFilenames);
- // changes the caching behavior of the index data
- void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
// ----------------------
// error handling
diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp
index 6e4a10f..6080b36 100644
--- a/src/api/BamReader.cpp
+++ b/src/api/BamReader.cpp
@@ -310,19 +310,6 @@ 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
diff --git a/src/api/BamReader.h b/src/api/BamReader.h
index 30c4d5f..fb9064d 100644
--- a/src/api/BamReader.h
+++ b/src/api/BamReader.h
@@ -99,8 +99,6 @@ class API_EXPORT BamReader {
bool OpenIndex(const std::string& indexFilename);
// sets a custom BamIndex on this reader
void SetIndex(BamIndex* index);
- // changes the caching behavior of the index data
- void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
// ----------------------
// error handling
diff --git a/src/api/internal/BamMultiReader_p.cpp b/src/api/internal/BamMultiReader_p.cpp
index 076f1bb..ecf2839 100644
--- a/src/api/internal/BamMultiReader_p.cpp
+++ b/src/api/internal/BamMultiReader_p.cpp
@@ -623,22 +623,6 @@ void BamMultiReaderPrivate::SetErrorString(const string& where, const string& wh
m_errorString = where + SEPARATOR + what;
}
-// sets the index caching mode on the readers
-void BamMultiReaderPrivate::SetIndexCacheMode(const BamIndex::IndexCacheMode mode) {
-
- // iterate over readers
- vector<MergeItem>::iterator readerIter = m_readers.begin();
- vector<MergeItem>::iterator readerEnd = m_readers.end();
- for ( ; readerIter != readerEnd; ++readerIter ) {
- MergeItem& item = (*readerIter);
- BamReader* reader = item.Reader;
- if ( reader == 0 ) continue;
-
- // set reader's index cache mode
- reader->SetIndexCacheMode(mode);
- }
-}
-
bool BamMultiReaderPrivate::SetRegion(const BamRegion& region) {
// NB: While it may make sense to track readers in which we can
diff --git a/src/api/internal/BamMultiReader_p.h b/src/api/internal/BamMultiReader_p.h
index 01d1230..9d001f5 100644
--- a/src/api/internal/BamMultiReader_p.h
+++ b/src/api/internal/BamMultiReader_p.h
@@ -70,7 +70,6 @@ class BamMultiReaderPrivate {
bool HasIndexes(void) const;
bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
bool OpenIndexes(const std::vector<std::string>& indexFilenames);
- void SetIndexCacheMode(const BamIndex::IndexCacheMode mode);
// error handling
std::string GetErrorString(void) const;
diff --git a/src/api/internal/BamRandomAccessController_p.cpp b/src/api/internal/BamRandomAccessController_p.cpp
index 1e44b7d..c223ed7 100644
--- a/src/api/internal/BamRandomAccessController_p.cpp
+++ b/src/api/internal/BamRandomAccessController_p.cpp
@@ -21,7 +21,6 @@ using namespace std;
BamRandomAccessController::BamRandomAccessController(void)
: m_index(0)
- , m_indexCacheMode(BamIndex::LimitedIndexCaching)
, m_hasAlignmentsInRegion(true)
{ }
@@ -174,11 +173,8 @@ bool BamRandomAccessController::CreateIndex(BamReaderPrivate* reader,
return false;
}
- // save new index
+ // save new index & return success
SetIndex(newIndex);
-
- // set new index's cache mode & return success
- newIndex->SetCacheMode(m_indexCacheMode);
return true;
}
@@ -226,9 +222,6 @@ bool BamRandomAccessController::OpenIndex(const string& indexFilename, BamReader
return false;
}
- // set cache mode
- index->SetCacheMode(m_indexCacheMode);
-
// attempt to load data from index file
if ( !index->Load(indexFilename) ) {
const string indexError = index->GetErrorString();
@@ -257,12 +250,6 @@ void BamRandomAccessController::SetIndex(BamIndex* index) {
m_index = index;
}
-void BamRandomAccessController::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) {
- m_indexCacheMode = mode;
- if ( m_index )
- m_index->SetCacheMode(mode);
-}
-
bool BamRandomAccessController::SetRegion(const BamRegion& region, const int& referenceCount) {
// store region
diff --git a/src/api/internal/BamRandomAccessController_p.h b/src/api/internal/BamRandomAccessController_p.h
index 43b6fb0..9262a61 100644
--- a/src/api/internal/BamRandomAccessController_p.h
+++ b/src/api/internal/BamRandomAccessController_p.h
@@ -55,7 +55,6 @@ class BamRandomAccessController {
bool LocateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& preferredType);
bool OpenIndex(const std::string& indexFilename, BamReaderPrivate* reader);
void SetIndex(BamIndex* index);
- void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
// region methods
void ClearRegion(void);
@@ -80,7 +79,6 @@ class BamRandomAccessController {
// index data
BamIndex* m_index; // owns the index, not a copy - responsible for deleting
- BamIndex::IndexCacheMode m_indexCacheMode;
// region data
BamRegion m_region;
diff --git a/src/api/internal/BamReader_p.cpp b/src/api/internal/BamReader_p.cpp
index 11cba33..dc6792f 100644
--- a/src/api/internal/BamReader_p.cpp
+++ b/src/api/internal/BamReader_p.cpp
@@ -447,11 +447,6 @@ void BamReaderPrivate::SetIndex(BamIndex* index) {
m_randomAccessController.SetIndex(index);
}
-// change the index caching behavior
-void BamReaderPrivate::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) {
- m_randomAccessController.SetIndexCacheMode(mode);
-}
-
// sets current region & attempts to jump to it
// returns success/failure
bool BamReaderPrivate::SetRegion(const BamRegion& region) {
diff --git a/src/api/internal/BamReader_p.h b/src/api/internal/BamReader_p.h
index 2f670d5..f928273 100644
--- a/src/api/internal/BamReader_p.h
+++ b/src/api/internal/BamReader_p.h
@@ -67,7 +67,6 @@ class BamReaderPrivate {
bool LocateIndex(const BamIndex::IndexType& preferredType);
bool OpenIndex(const std::string& indexFilename);
void SetIndex(BamIndex* index);
- void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
// error handling
std::string GetErrorString(void) const;
diff --git a/src/api/internal/BamStandardIndex_p.cpp b/src/api/internal/BamStandardIndex_p.cpp
index c492899..8b23f74 100644
--- a/src/api/internal/BamStandardIndex_p.cpp
+++ b/src/api/internal/BamStandardIndex_p.cpp
@@ -62,7 +62,6 @@ BamStandardIndex::RaiiWrapper::~RaiiWrapper(void) {
// ctor
BamStandardIndex::BamStandardIndex(Internal::BamReaderPrivate* reader)
: BamIndex(reader)
- , m_cacheMode(BamIndex::LimitedIndexCaching)
, m_bufferLength(0)
{
m_isBigEndian = BamTools::SystemIsBigEndian();
@@ -762,12 +761,6 @@ void BamStandardIndex::Seek(const int64_t& position, const int& origin) {
throw BamException("BamStandardIndex::Seek", "could not seek in BAI file");
}
-// change the index caching behavior
-void BamStandardIndex::SetCacheMode(const BamIndex::IndexCacheMode& mode) {
- m_cacheMode = mode;
- // do nothing else here ? cache mode will be ignored from now on, most likely
-}
-
void BamStandardIndex::SkipBins(const int& numBins) {
uint32_t binId;
int32_t numAlignmentChunks;
diff --git a/src/api/internal/BamStandardIndex_p.h b/src/api/internal/BamStandardIndex_p.h
index cb907ac..03e0042 100644
--- a/src/api/internal/BamStandardIndex_p.h
+++ b/src/api/internal/BamStandardIndex_p.h
@@ -122,8 +122,6 @@ class BamStandardIndex : public BamIndex {
bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion);
// loads existing data from file into memory
bool Load(const std::string& filename);
- // change the index caching behavior
- void SetCacheMode(const BamIndex::IndexCacheMode& mode);
public:
// returns format's file extension
static const std::string Extension(void);
@@ -198,7 +196,6 @@ class BamStandardIndex : public BamIndex {
// data members
private:
bool m_isBigEndian;
- BamIndex::IndexCacheMode m_cacheMode;
BaiFileSummary m_indexFileSummary;
// our input buffer
diff --git a/src/api/internal/BamToolsIndex_p.cpp b/src/api/internal/BamToolsIndex_p.cpp
index 567b551..cdf3d10 100644
--- a/src/api/internal/BamToolsIndex_p.cpp
+++ b/src/api/internal/BamToolsIndex_p.cpp
@@ -53,7 +53,6 @@ BamToolsIndex::RaiiWrapper::~RaiiWrapper(void) {
// ctor
BamToolsIndex::BamToolsIndex(Internal::BamReaderPrivate* reader)
: BamIndex(reader)
- , m_cacheMode(BamIndex::LimitedIndexCaching)
, m_blockSize(BamToolsIndex::DEFAULT_BLOCK_LENGTH)
, m_inputVersion(0)
, m_outputVersion(BTI_2_0) // latest version - used for writing new index files
@@ -538,12 +537,6 @@ void BamToolsIndex::Seek(const int64_t& position, const int& origin) {
throw BamException("BamToolsIndex::Seek", "could not seek in BAI file");
}
-// change the index caching behavior
-void BamToolsIndex::SetCacheMode(const BamIndex::IndexCacheMode& mode) {
- m_cacheMode = mode;
- // do nothing else here ? cache mode will be ignored from now on, most likely
-}
-
void BamToolsIndex::SkipBlocks(const int& numBlocks) {
Seek( numBlocks*BamToolsIndex::SIZEOF_BLOCK, SEEK_CUR );
}
diff --git a/src/api/internal/BamToolsIndex_p.h b/src/api/internal/BamToolsIndex_p.h
index 902be79..7c1550b 100644
--- a/src/api/internal/BamToolsIndex_p.h
+++ b/src/api/internal/BamToolsIndex_p.h
@@ -117,8 +117,6 @@ class BamToolsIndex : public BamIndex {
bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion);
// loads existing data from file into memory
bool Load(const std::string& filename);
- // change the index caching behavior
- void SetCacheMode(const BamIndex::IndexCacheMode& mode);
public:
// returns format's file extension
static const std::string Extension(void);
@@ -160,7 +158,6 @@ class BamToolsIndex : public BamIndex {
// data members
private:
bool m_isBigEndian;
- BamIndex::IndexCacheMode m_cacheMode;
BtiFileSummary m_indexFileSummary;
uint32_t m_blockSize;
int32_t m_inputVersion; // Version is serialized as int
--
2.39.5