Fixed chromId bug, removed debug metric from RecordOutputMgr

src/utils/Contexts/Context.cpp

@@ -111,6 +111,10 @@ bool Context::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
 		}
 
 		if (strcmp(argv[i], "-i") == 0) {
+			if (argc <= i+1) {
+				_errorMsg = "Error: -i option given, but no input file specified.";
+				return false;
+			}
 			addInputFile(argv[i+1]);
 			markUsed(i - skipFirstArgs);
 			i++;

src/utils/FileRecordTools/FileRecordMgr.cpp

@@ -133,9 +133,8 @@ Record *FileRecordMgr::allocateAndGetNextRecord()
 	//test for sorted order, if necessary.
 	if (_context->getSortedInput()) {
 		testInputSortOrder(record);
-	} else {
-		assignChromId(record);
 	}
+	assignChromId(record);
 	_totalRecordLength += (unsigned long)(record->getEndPos() - record->getStartPos());
 	return record;
 }

src/utils/FileRecordTools/RecordOutputMgr.cpp

@@ -28,8 +28,7 @@ RecordOutputMgr::RecordOutputMgr()
 : _context(NULL),
   _printable(true),
   _bamWriter(NULL),
-  _currBlockList(NULL),
-  _numWrites(0)
+  _currBlockList(NULL)
 {
 
 }
@@ -38,9 +37,7 @@ RecordOutputMgr::~RecordOutputMgr()
 {
 	if (_outBuf.size() > 0) {
 		flush();
-		_numWrites++;
 	}
-	cerr << "Total number of buffer writes was " << _numWrites << endl;
 	if (_bamWriter != NULL) {
 		_bamWriter->Close();
 		delete _bamWriter;
@@ -112,7 +109,6 @@ void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockLi
 {
 	if (needsFlush()) {
 		flush();
-		_numWrites++;
 	}
 
 	//The first time we print a record is when we print any header, because the header

src/utils/FileRecordTools/RecordOutputMgr.h

@@ -40,7 +40,6 @@ private:
 	RecordKeyList *_currBlockList;
 
 	QuickString _outBuf;
-	int _numWrites;
 
 	//some helper functions to neaten the code.
 	void tab() { _outBuf.append('\t'); }