Merge pull request #244 from nkindlon/master

Removed accidental copy in BinTree to fix speed

src/closestFile/closestHelp.cpp

@@ -73,6 +73,7 @@ void closest_help(void) {
     cerr                        << "\t\tFor BED, the 4th column is compared." << endl << endl;
 
     IntersectCommonHelp();
+    multiDbOutputHelp();
     allToolsCommonHelp();
 
     cerr << "Notes: " << endl;

src/intersectFile/intersectHelp.cpp

@@ -33,6 +33,7 @@ void intersect_help(void) {
     IntersectCommonHelp();
 
     sortedHelp();
+    multiDbOutputHelp();
     allToolsCommonHelp();
 
     cerr << "Notes: " << endl;

src/utils/BinTree/BinTree.cpp

@@ -57,17 +57,14 @@ void BinTree::getHits(Record *record, RecordKeyVector &hitSet)
 		return;
 	}
 
-    binNumType startBin = 0;
-    binNumType endBin = 0;
-
     binNumType startPos = record->getStartPos();
     binNumType endPos = record->getEndPos();
 
-    startBin = (startPos >> _binFirstShift);
-    endBin = ((endPos-1) >> _binFirstShift);
+    binNumType startBin = (startPos >> _binFirstShift);
+    binNumType endBin = ((endPos-1) >> _binFirstShift);
 
 
-	const allBinsType bins = mainIter->second;
+	const allBinsType &bins = mainIter->second;
 
     /* SYNOPSIS:
          1. We loop through each UCSC BIN level for feature A's chrom.

src/utils/general/CommonHelp.cpp

@@ -69,7 +69,12 @@ void IntersectCommonHelp() {
     cerr << "\t-g\t"       		<< "Provide a genome file to enforce consistent chromosome sort order" << endl;
     cerr 						<<"\t\tacross input files. Only applies when used with -sorted option." << endl << endl;
 
+    cerr << "\t-nonamecheck\t"       << "For sorted data, don't throw an error if the file has different naming conventions" << endl;
+    cerr							<< "\t\t\tfor the same chromosome. ex. \"chr1\" vs \"chr01\"." << endl << endl;
+
+}
 
+void multiDbOutputHelp() {
     cerr << "\t-names\t"       << "When using multiple databases, provide an alias for each that" << endl;
     cerr						<<"\t\twill appear instead of a fileId when also printing the DB record." << endl << endl;
 
@@ -78,10 +83,6 @@ void IntersectCommonHelp() {
 
     cerr << "\t-sortout\t"       << "When using multiple databases, sort the output DB hits" << endl;
     cerr						<< "\t\t\tfor each record." << endl << endl;
-
-    cerr << "\t-nonamecheck\t"       << "For sorted data, don't throw an error if the file has different naming conventions" << endl;
-    cerr							<< "\t\t\tfor the same chromosome. ex. \"chr1\" vs \"chr01\"." << endl << endl;
-
 }
 
 

src/utils/general/CommonHelp.h

@@ -18,5 +18,6 @@ extern void allToolsCommonHelp();
 extern void IntersectCommonHelp();
 extern void IntersectOutputHelp();
 extern void sortedHelp();
+extern void multiDbOutputHelp();
 
 #endif /* COMMONHELPFILE_H_ */