Closed chromosome name string memory leak

TODO.txt

@@ -1,7 +1,6 @@
 Hold fire on writers
 Seekable apply_paste
-Memory tracking & cleaning of chrom labels
-Read strand in BigBed files?
+Memory tracking & cleaning of chrom labels for text files
 Read score in BigBed files? => Handling overlapping iterators with value in unit and filter
 Read data in VCF file?
 HMM app? (requires reverse iterators...)

src/apply.c

@@ -277,9 +277,7 @@ void computeApplyValues(Multiplexer * apply, ApplyMultiplexerData * data, Buffer
 			apply->values[i] = *((double*) (wi->data));
 			WiggleIterator * tmp = wi;
 			wi = wi->append;
-			if (tmp->data)
-				free(tmp->data);
-			free(tmp);
+			destroyWiggleIterator(tmp);
 			i++;
 		}
 	} else

src/bedReader.c

@@ -120,7 +120,7 @@ WiggleIterator * BedReader(char * filename) {
 		fprintf(stderr, "Could not open bed file %s\n", filename);
 		exit(1);
 	}
-	WiggleIterator * res = newWiggleIterator(data, &BedReaderPop, &BedReaderSeek, 0);
+	WiggleIterator * res = newWiggleIteratorChromName(data, &BedReaderPop, &BedReaderSeek, 0);
 	res->overlaps = true;
 	return res;
 }

src/samReader.c

@@ -222,5 +222,5 @@ WiggleIterator * SamReader(char * filename) {
 		}
 	} else
 		data->file = stdin;
-	return newWiggleIterator(data, &SamReaderPop, &SamReaderSeek, 0);
+	return newWiggleIteratorChromName(data, &SamReaderPop, &SamReaderSeek, 0);
 }

src/unaryOps.c

@@ -306,7 +306,7 @@ void CoverageWiggleIteratorPop(WiggleIterator * wi) {
 	CoverageWiggleIteratorData * data = (CoverageWiggleIteratorData *) wi->data;
 	WiggleIterator * iter = data->iter;
 	if (!iter->done) {
-		if (wi->chrom[0] == '\0')
+		if (wi->chrom == NULL)
 			wi->value = 0;
 
 		while (fh_notempty(data->heap) && fh_min(data->heap) == wi->finish) {

src/vcfReader.c

@@ -95,7 +95,7 @@ WiggleIterator * VcfReader(char * filename) {
 		fprintf(stderr, "Could not open bed file %s\n", filename);
 		exit(1);
 	}
-	WiggleIterator * res = newWiggleIterator(data, &VcfReaderPop, &VcfReaderSeek, 0);
+	WiggleIterator * res = newWiggleIteratorChromName(data, &VcfReaderPop, &VcfReaderSeek, 0);
 	res->value = 1;
 	res->overlaps = true;
 	return res;

src/wigReader.c

@@ -245,5 +245,5 @@ WiggleIterator * WiggleReader(char * f) {
 		data->file = stdin;
 	data->readingMode = BED_GRAPH;
 	data->stop = -1;
-	return CompressionWiggleIterator(newWiggleIterator(data, &WiggleReaderPop, &WiggleReaderSeek, 0));
+	return CompressionWiggleIterator(newWiggleIteratorChromName(data, &WiggleReaderPop, &WiggleReaderSeek, 0));
 }	

src/wiggleIterator.c

@@ -18,6 +18,22 @@
 #include "wiggleIterator.h"
 
 WiggleIterator * newWiggleIterator(void * data, void (*popFunction)(WiggleIterator *), void (*seek)(WiggleIterator *, const char *, int, int), double default_value) {
+	WiggleIterator * new = (WiggleIterator *) calloc(1, sizeof(WiggleIterator));
+	new->data = data;
+	new->pop = popFunction;
+	new->seek = seek;
+	new->chrom = NULL;
+	new->value = 1; // Default value for non-valued bed tracks;
+	new->strand = 0; // Default value for non-stranded data;
+	new->valuePtr = NULL;
+	new->overlaps = false;
+	new->append = NULL;
+	new->default_value = default_value;
+	pop(new);
+	return new;
+}
+
+WiggleIterator * newWiggleIteratorChromName(void * data, void (*popFunction)(WiggleIterator *), void (*seek)(WiggleIterator *, const char *, int, int), double default_value) {
 	WiggleIterator * new = (WiggleIterator *) calloc(1, sizeof(WiggleIterator));
 	new->data = data;
 	new->pop = popFunction;
@@ -35,7 +51,6 @@ WiggleIterator * newWiggleIterator(void * data, void (*popFunction)(WiggleIterat
 
 void destroyWiggleIterator(WiggleIterator * wi) {
 	free(wi->data);
-	free(wi->chrom);
 	free(wi);
 }
 

src/wiggleIterator.h

@@ -35,6 +35,7 @@ struct wiggleIterator_st {
 };
 
 WiggleIterator * newWiggleIterator(void * data, void (*pop)(WiggleIterator *), void (*seek)(WiggleIterator *, const char *, int, int), double default_value);
+WiggleIterator * newWiggleIteratorChromName(void * data, void (*popFunction)(WiggleIterator *), void (*seek)(WiggleIterator *, const char *, int, int), double default_value);
 void pop(WiggleIterator *);
 WiggleIterator * CompressionWiggleIterator(WiggleIterator *);