Merge branch 'master' of https://github.com/nkindlon/bedtools2

src/closestFile/closestMain.cpp

@@ -114,6 +114,11 @@ void closest_help(void) {
 
     cerr << "\t-header\t"       << "Print the header from the A file prior to results." << 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;
+
+
+
     cerr << "Notes: " << endl;
     cerr << "\tReports \"none\" for chrom and \"-1\" for all other fields when a feature" << endl;
     cerr << "\tis not found in B on the same chromosome as the feature in A." << endl;

src/jaccard/jaccardMain.cpp

@@ -73,6 +73,11 @@ void jaccard_help(void) {
     cerr << "\t\t"			   << "the forward or reverse strand, respectively." << endl;
     cerr << "\t\t"			   << "- By default, merging is done without respect to strand." << 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;
+
+
+
     cerr << "Notes: " << endl;
     cerr << "\t(1) Input files must be sorted by chrom, then start position."
          << endl << endl;

src/mapFile/mapMain.cpp

@@ -84,6 +84,10 @@ void map_help(void) {
 
     cerr << "\t-prec\t"   		 << "Sets the decimal precision for output (Default: 5)" << 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;
+
+
 
     cerr << "Notes: " << endl;
     cerr << "\t(1) Both input files must be sorted by chrom, then start." << endl << endl;

src/utils/Contexts/ContextBase.cpp

@@ -60,7 +60,8 @@ ContextBase::ContextBase()
   _useMergedIntervals(false),
   _reportPrecision(-1),
   _allFilesHaveChrInChromNames(UNTESTED),
-  _allFileHaveLeadingZeroInChromNames(UNTESTED)
+  _allFileHaveLeadingZeroInChromNames(UNTESTED),
+  _nameConventionWarningTripped(false)
 
 {
 	_programNames["intersect"] = INTERSECT;
@@ -92,6 +93,12 @@ ContextBase::~ContextBase()
 		_keyListOps = NULL;
 	}
 
+	// if there was a warning about file name conventions,
+	// print it again so it's not lost amid large output.
+	if (_nameConventionWarningTripped) {
+		cerr << _nameConventionWarningMsg << endl;
+	}
+
 }
 
 bool ContextBase::determineOutputType() {
@@ -626,7 +633,7 @@ bool ContextBase::parseIoBufSize(QuickString bufStr)
 }
 
 void ContextBase::testNameConventions(const Record *record) {
-	if (getNameCheckDisabled()) return;
+	if (getNameCheckDisabled() || _nameConventionWarningTripped) return;
 
 	int fileIdx = record->getFileIdx();
 
@@ -639,15 +646,12 @@ void ContextBase::testNameConventions(const Record *record) {
 
 	if (testChrVal == UNTESTED) {
 		_fileHasChrInChromNames[fileIdx] = hasChr ? YES : NO;
-	} else if ((testChrVal == YES && !hasChr) || (testChrVal == NO && hasChr)) {
-		fprintf(stderr, "ERROR: File %s has inconsistent naming convention for record:\n", _fileNames[fileIdx].c_str());
-		record->print(stderr, true);
-		exit(1);
 	}
+//	else if ((testChrVal == YES && !hasChr) || (testChrVal == NO && hasChr)) {
+//		nameConventionWarning(record, _fileNames[fileIdx], " has inconsistent naming convention for record:\n");
+//	}
 	if ((_allFilesHaveChrInChromNames == YES && !hasChr) || (_allFilesHaveChrInChromNames == NO && hasChr)) {
-		fprintf(stderr, "ERROR: File %s has a record where naming convention is inconsistent with other files:\n", _fileNames[fileIdx].c_str());
-		record->print(stderr, true);
-		exit(1);
+		nameConventionWarning(record, _fileNames[fileIdx], " has a record where naming convention is inconsistent with other files:\n");
 	}
 
 	if (_allFilesHaveChrInChromNames == UNTESTED) {
@@ -664,15 +668,12 @@ void ContextBase::testNameConventions(const Record *record) {
 	testChrVal = fileHasLeadingZeroInChromNames(fileIdx);
 	if (testChrVal == UNTESTED) {
 		_fileHasLeadingZeroInChromNames[fileIdx] = zeroVal ? YES : NO;
-	} else if ((testChrVal == YES && !zeroVal) || (testChrVal == NO && zeroVal)) {
-		fprintf(stderr, "ERROR: File %s has inconsistent naming convention (leading zero) for record:\n", _fileNames[fileIdx].c_str());
-		record->print(stderr, true);
-		exit(1);
 	}
+//	else if ((testChrVal == YES && !zeroVal) || (testChrVal == NO && zeroVal)) {
+//		nameConventionWarning(record, _fileNames[fileIdx], " has inconsistent naming convention (leading zero) for record:\n");
+//	}
 	if ((_allFileHaveLeadingZeroInChromNames == YES && !zeroVal) || (_allFileHaveLeadingZeroInChromNames == NO && zeroVal)) {
-		fprintf(stderr, "ERROR: File %s has a record where naming convention (leading zero) is inconsistent with other files:\n", _fileNames[fileIdx].c_str());
-		record->print(stderr, true);
-		exit(1);
+		nameConventionWarning(record, _fileNames[fileIdx], " has a record where naming convention (leading zero) is inconsistent with other files:\n");
 	}
 
 	if (_allFileHaveLeadingZeroInChromNames == UNTESTED) {
@@ -696,3 +697,15 @@ ContextBase::testType ContextBase::fileHasLeadingZeroInChromNames(int fileIdx) {
 	return iter->second;
 }
 
+void ContextBase::nameConventionWarning(const Record *record, const QuickString &filename, const QuickString &message)
+{
+	_nameConventionWarningMsg = "***** WARNING: File ";
+	_nameConventionWarningMsg.append(filename);
+	_nameConventionWarningMsg.append(message);
+	record->print(_nameConventionWarningMsg);
+	_nameConventionWarningMsg.append("\n");
+	_nameConventionWarningTripped = true;
+
+	cerr << _nameConventionWarningMsg << endl;
+}
+

src/utils/Contexts/ContextBase.h

@@ -277,6 +277,12 @@ protected:
 
     testType _allFilesHaveChrInChromNames;
     testType _allFileHaveLeadingZeroInChromNames;
+
+    //Warning messages.
+    bool _nameConventionWarningTripped;
+    QuickString _nameConventionWarningMsg;
+    void nameConventionWarning(const Record *record, const QuickString &filename, const QuickString &message);
+
 };
 
 #endif /* CONTEXTBASE_H_ */

src/utils/Contexts/ContextIntersect.cpp

@@ -168,10 +168,6 @@ bool ContextIntersect::isValidState()
 	if (_files.size()  < 2 ) {
 		return false;
 	}
-	if (!getSortedInput() && getNameCheckDisabled()) {
-		_errorMsg = "\n***** ERROR: -nonamecheck option is only valid for sorted input. *****";
-		return false;
-	}
 	return true;
 }
 

test/intersect/sortAndNaming/test-sort-and-naming.sh

@@ -74,9 +74,9 @@ rm obs
 ############################################################
 echo "    intersect.t05...\c"
 echo \
-"ERROR: File db1_noChr.bed has inconsistent naming convention for record:
+"***** WARNING: File db1_noChr.bed has inconsistent naming convention for record:
 2	50	80" > exp
-$BT intersect -a q1_num.bed -b db1_noChr.bed  -sorted 2>&1 > /dev/null | cat - > obs
+$BT intersect -a q1_num.bed -b db1_noChr.bed  -sorted 2>&1 > /dev/null | cat - | head -2 > obs
 check obs exp
 rm obs
 
@@ -86,9 +86,9 @@ rm obs
 ############################################################
 echo "    intersect.t06...\c"
 echo \
-"ERROR: File db1_leadingZero.txt has a record where naming convention (leading zero) is inconsistent with other files:
+"***** WARNING: File db1_leadingZero.txt has a record where naming convention (leading zero) is inconsistent with other files:
 chr01	10	20" > exp
-$BT intersect -a q1_num.bed -b db1_leadingZero.txt -sorted 2>&1 > /dev/null | cat - > obs
+$BT intersect -a q1_num.bed -b db1_leadingZero.txt -sorted 2>&1 > /dev/null | head -2 > obs
 check obs exp
 rm obs
 

test/intersect/test-intersect.sh

@@ -554,9 +554,9 @@ echo ok
 ##################################################################
 echo "    intersect.t45...\c"
 echo \
-"ERROR: File nonamecheck_b.bed has a record where naming convention (leading zero) is inconsistent with other files:
+"***** WARNING: File nonamecheck_b.bed has a record where naming convention (leading zero) is inconsistent with other files:
 chr01	15	25" > exp
-$BT intersect -a nonamecheck_a.bed -b nonamecheck_b.bed -sorted 2>&1 > /dev/null | cat - > obs
+$BT intersect -a nonamecheck_a.bed -b nonamecheck_b.bed -sorted 2>&1 > /dev/null | cat - | head -2 > obs
 check exp obs
 rm exp obs