From a12d9422b9eab8fdd46eb9444dde3ea5abebf551 Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Mon, 16 Dec 2013 15:44:39 -0500
Subject: [PATCH] ifdef'd out DualQueue and removed usages of it to fix
compiler errors with clang on Mac OS X
---
.../FileReaders/InputStreamMgr.cpp | 2 +-
src/utils/FileRecordTools/FileRecordMgr.cpp | 8 ++++++--
src/utils/FileRecordTools/FileRecordMgr.h | 19 ++++++++++---------
src/utils/NewChromsweep/NewChromsweep.cpp | 16 ++++++++--------
src/utils/general/DualQueue.h | 3 ++-
test/sample/test-sample.sh | 2 +-
6 files changed, 28 insertions(+), 22 deletions(-)
diff --git a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
index 073e4858..1f9d0441 100644
--- a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
+++ b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
@@ -280,7 +280,7 @@ void InputStreamMgr::readZipChunk()
size_t numCharsRead = read(_tmpZipBuf, (size_t)SCAN_BUFFER_SIZE);
_saveDataStr.append(_tmpZipBuf);
_numBytesInBuffer = _saveDataStr.size();
- if (numCharsRead < SCAN_BUFFER_SIZE) {
+ if ((int)numCharsRead < SCAN_BUFFER_SIZE) {
_streamFinished = true;
}
return;
diff --git a/src/utils/FileRecordTools/FileRecordMgr.cpp b/src/utils/FileRecordTools/FileRecordMgr.cpp
index 5d632635..113b5efa 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.cpp
+++ b/src/utils/FileRecordTools/FileRecordMgr.cpp
@@ -103,7 +103,8 @@ void FileRecordMgr::close(){
}
bool FileRecordMgr::eof(){
- return _storedRecords.empty() && _fileReader->eof() ? true: false;
+ return _fileReader->eof();
+// return _storedRecords.empty() && _fileReader->eof() ? true: false;
}
Record *FileRecordMgr::allocateAndGetNextRecord()
@@ -235,6 +236,9 @@ void FileRecordMgr::allocateFileReader()
}
}
+
+#ifdef false
+
Record *FileRecordMgr::allocateAndGetNextMergedRecord(WANT_STRAND_TYPE desiredStrand, int maxDistance) {
RecordKeyList recList;
if (!allocateAndGetNextMergedRecord(recList, desiredStrand, maxDistance)) {
@@ -403,4 +407,4 @@ void FileRecordMgr::deleteAllMergedItemsButKey(RecordKeyList &recList) {
}
recList.clearList();
}
-
+#endif
diff --git a/src/utils/FileRecordTools/FileRecordMgr.h b/src/utils/FileRecordTools/FileRecordMgr.h
index a3ef2877..3dc61d1c 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.h
+++ b/src/utils/FileRecordTools/FileRecordMgr.h
@@ -13,7 +13,7 @@ using namespace std;
#include <string>
#include "QuickString.h"
#include <set>
-#include "DualQueue.h"
+//#include "DualQueue.h"
//include headers for all FileReader and derivative classes.
#include "Context.h"
@@ -80,7 +80,7 @@ public:
Record *allocateAndGetNextRecord();
void deleteRecord(const Record *);
-
+#ifdef false
//////////////////////////////////////////////////////////////////////////////////
//
// MERGED RECORDS
@@ -121,7 +121,7 @@ public:
// END MERGED RECORDS
//
//////////////////////////////////////////////////////////////////////////////////
-
+#endif
//File statistics
unsigned long getTotalRecordLength() const { return _totalRecordLength; } //sum of length of all returned records
@@ -161,7 +161,7 @@ private:
int _prevChromId;
//members for handling merged records
- DualQueue<Record *, DualQueueAscending > _storedRecords;
+// DualQueue<Record *, DualQueueAscending > _storedRecords;
bool _mustBeForward;
bool _mustBeReverse;
@@ -178,11 +178,6 @@ private:
void testInputSortOrder(Record *record);
void assignChromId(Record *);
void sortError(const Record *record, bool genomeFileError);
-
- void deleteAllMergedItemsButKey(RecordKeyList &recList);
- void addToStorage(Record *record);
- Record *tryToTakeFromStorage();
- Record *tryToTakeFromStorage(bool strand);
void testBufferedMgr() const {
if (_bufStreamMgr == NULL) {
cerr << "Error: attempted to access type information for file " << _context->getInputFileName(_contextFileIdx) << " before it was opened." << endl;
@@ -190,6 +185,12 @@ private:
}
}
+#ifdef false
+ void deleteAllMergedItemsButKey(RecordKeyList &recList);
+ void addToStorage(Record *record);
+ Record *tryToTakeFromStorage();
+ Record *tryToTakeFromStorage(bool strand);
+#endif
};
diff --git a/src/utils/NewChromsweep/NewChromsweep.cpp b/src/utils/NewChromsweep/NewChromsweep.cpp
index 27cc4b92..e095a1a5 100644
--- a/src/utils/NewChromsweep/NewChromsweep.cpp
+++ b/src/utils/NewChromsweep/NewChromsweep.cpp
@@ -197,20 +197,20 @@ bool NewChromSweep::next(RecordKeyList &next) {
void NewChromSweep::nextRecord(bool query) {
if (query) {
- if (!_context->getUseMergedIntervals()) {
+// if (!_context->getUseMergedIntervals()) {
_currQueryRec = _queryFRM->allocateAndGetNextRecord();
- } else {
- _currQueryRec = _queryFRM->allocateAndGetNextMergedRecord(_context->getSameStrand() ? FileRecordMgr::SAME_STRAND_EITHER : FileRecordMgr::ANY_STRAND);
- }
+// } else {
+// _currQueryRec = _queryFRM->allocateAndGetNextMergedRecord(_context->getSameStrand() ? FileRecordMgr::SAME_STRAND_EITHER : FileRecordMgr::ANY_STRAND);
+// }
if (_currQueryRec != NULL) {
_queryRecordsTotalLength += (unsigned long)(_currQueryRec->getEndPos() - _currQueryRec->getStartPos());
}
} else { //database
- if (!_context->getUseMergedIntervals()) {
+// if (!_context->getUseMergedIntervals()) {
_currDatabaseRec = _databaseFRM->allocateAndGetNextRecord();
- } else {
- _currDatabaseRec = _databaseFRM->allocateAndGetNextMergedRecord(_context->getSameStrand() ? FileRecordMgr::SAME_STRAND_EITHER : FileRecordMgr::ANY_STRAND);
- }
+// } else {
+// _currDatabaseRec = _databaseFRM->allocateAndGetNextMergedRecord(_context->getSameStrand() ? FileRecordMgr::SAME_STRAND_EITHER : FileRecordMgr::ANY_STRAND);
+// }
if (_currDatabaseRec != NULL) {
_databaseRecordsTotalLength += (unsigned long)(_currDatabaseRec->getEndPos() - _currDatabaseRec->getStartPos());
}
diff --git a/src/utils/general/DualQueue.h b/src/utils/general/DualQueue.h
index ccc8b7b0..1cee4158 100644
--- a/src/utils/general/DualQueue.h
+++ b/src/utils/general/DualQueue.h
@@ -4,7 +4,7 @@
* Created on: Jan 29, 2013
* Author: nek3d
*/
-
+#ifdef false
#ifndef DUALQUEUE_H_
#define DUALQUEUE_H_
@@ -121,3 +121,4 @@ private:
#endif /* DUALQUEUE_H_ */
+#endif
diff --git a/test/sample/test-sample.sh b/test/sample/test-sample.sh
index 9cae9bc0..5a65085c 100644
--- a/test/sample/test-sample.sh
+++ b/test/sample/test-sample.sh
@@ -91,7 +91,7 @@ rm obs exp
# Test that we get the requested number of records
############################################################
echo " sample.new.t07...\c"
-echo " 10" > exp
+echo "10" > exp
$BT sample -i mainFile.bed -n 10 | wc -l > obs
check obs exp
#rm obs exp
--
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