Testing accuracy of seek, and correcting for off by one errors

JiahuaQu · Jan 7, 2021 · 8f7b9a2 · 8f7b9a2
1 parent af94ce0
commit 8f7b9a2
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Showing 3 changed files with 20 additions and 4 deletions.
diff --git a/src/bigBedReader.c b/src/bigBedReader.c
@@ -43,7 +43,8 @@ static int readIteratorEntries(bwOverlapIterator_t *iter, char * chrom, int stre
 }
 
 static int readBigBedRegion(BigBedReaderData * data, char * chrom, int start, int stop) {
-	bwOverlapIterator_t *iter = bbOverlappingEntriesIterator(data->fp, chrom, start, stop, 0, MAX_BLOCKS);
+	// BigBed format 1 indexed, hence the -1s
+	bwOverlapIterator_t *iter = bbOverlappingEntriesIterator(data->fp, chrom, start - 1, stop - 1, 0, MAX_BLOCKS);
 	if (!iter)
 		return 0;
 
@@ -74,7 +75,7 @@ void * readBigBed(void * ptr) {
 		qsort(chrom_lengths, data->fp->cl->nKeys, sizeof(Chrom_length), compare_chrom_lengths);
 
 		for (chrom_index = 0; chrom_index < data->fp->cl->nKeys; chrom_index++)
-			if (readBigBedRegion(data, chrom_lengths[chrom_index].chrom, 0, chrom_lengths[chrom_index].length))
+			if (readBigBedRegion(data, chrom_lengths[chrom_index].chrom, 1, chrom_lengths[chrom_index].length))
 				break;
 
 		free(chrom_lengths);

diff --git a/src/bigWiggleReader.c b/src/bigWiggleReader.c
@@ -50,7 +50,7 @@ static int readIteratorIntervals(bwOverlapIterator_t *iter, char * chrom, int st
 }
 
 static int readBigWiggleRegion(BigWiggleReaderData * data, char * chrom, int start, int stop) {
-	bwOverlapIterator_t *iter = bwOverlappingIntervalsIterator(data->fp, chrom, start, stop, MAX_BLOCKS);
+	bwOverlapIterator_t *iter = bwOverlappingIntervalsIterator(data->fp, chrom, start - 1, stop - 1, MAX_BLOCKS);
 	if (!iter)
 		return 0;
 
@@ -69,7 +69,7 @@ static int readBigWiggleChromosome(BigWiggleReaderData * data, char * chrom, int
 	int start;
 	int stretch=10000;
 
-	for (start = 0; start < length; start+=stretch) {
+	for (start = 1; start < length; start+=stretch) {
 		if (readBigWiggleRegion(data, chrom, start, start+stretch))
 			return 1;
 	}

diff --git a/test/test.py b/test/test.py
@@ -51,6 +51,21 @@ def testOutput(cmd):
 # Testing VCF and BCF
 assert test('../bin/wiggletools do isZero diff vcf.vcf bcf.bcf') == 0
 
+# Testing BAM & BedGraph
+assert test('../bin/wiggletools do isZero seek GL000200.1 1 1000 diff bam.bam pileup.bg') == 0
+
+# Testing BAM & CRAM
+assert test('../bin/wiggletools do isZero seek GL000200.1 1 1000 diff bam.bam cram.cram') == 0
+
+# Testing Bed and BigBed
+assert test('../bin/wiggletools do isZero seek chr1 2 6 diff overlapping.bed overlapping.bb') == 0
+
+# Testing Wig and BigWig
+assert test('../bin/wiggletools do isZero seek chr1 2 6 diff variableStep.bw variableStep.wig') == 0
+
+# Testing VCF and BCF
+assert test('../bin/wiggletools do isZero seek chr1 2 6 diff vcf.vcf bcf.bcf') == 0
+
 # Testing sum, scale and multiplexers
 assert test('../bin/wiggletools do isZero diff sum fixedStep.bw fixedStep.bw : scale 2 fixedStep.bw') == 0