Merge pull request #4 from nkindlon/master

ifdef'd out DualQueue and removed usages of it to fix compiler errors wi...

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;

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

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
 
 
 };

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());
 		}

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

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