Read VCF struct vars length from SVLEN tag instead of using length of varRef field

src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp

@@ -137,3 +137,20 @@ bool SingleLineDelimTextFileReader::findDelimiters() {
 	}
 	return true;
 }
+
+int SingleLineDelimTextFileReader::getVcfSVlen() {
+	int startPos = _delimPositions[VCF_TAG_FIELD] +1;
+	const char *startPtr = strstr(_sLine.c_str() + startPos, "SVLEN=") +6;
+	const char *endPtr = strchr(startPtr, ';');
+	const char *midPtr = strchr(startPtr, ',');
+	int endCoord = -1;
+	if (midPtr != NULL && midPtr < endPtr) {
+		//comma found in the number, that means there are two numbers
+		int num1 = str2chrPos(startPtr, midPtr - startPtr);
+		int num2 = str2chrPos(midPtr +1, endPtr - (midPtr +1));
+		endCoord = max(abs(num1), abs(num2));
+	} else {
+		endCoord = abs(str2chrPos(startPtr, endPtr - startPtr));
+	}
+	return endCoord;
+}

src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h

@@ -15,6 +15,10 @@ using namespace std;
 
 class SingleLineDelimTextFileReader : public FileReader {
 public:
+	//Allow VCF records to access a specialized private method.
+	//See end of class declaration for details.
+	friend class VcfRecord;
+
 	SingleLineDelimTextFileReader(int numFields, char delimChar = '\t');
 	~SingleLineDelimTextFileReader();
 
@@ -26,6 +30,8 @@ public:
 	virtual void appendField(int fieldNum, QuickString &str) const;
 	virtual const QuickString &getHeader() const { return _header; }
 	virtual bool hasHeader() const { return _fullHeaderFound; }
+
+
 protected:
 	int _numFields;
 	char _delimChar;
@@ -40,6 +46,12 @@ protected:
 	bool detectAndHandleHeader();
 	bool findDelimiters();
 
+	//This is actually a very specialized function strictly for VCF
+	//records to read and process extra information about Structural Variants.
+	static const int VCF_TAG_FIELD = 7;
+	int getVcfSVlen();
+
+
 };
 
 

src/utils/FileRecordTools/Records/VcfRecord.cpp

@@ -18,13 +18,17 @@ bool VcfRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
 	_startPos--; // VCF is one-based. Here we intentionally don't decrement the string version,
 	//because we'll still want to output the one-based number in the print methods, even though
 	//internally we decrement the integer to comply with the 0-based format common to other records.
+	fileReader->getField(4, _varRef);
 	fileReader->getField(3, _varAlt);
-	//endPos is just the startPos plus the length of the variant
-	_endPos = _startPos + _varAlt.size();
+	if (_varRef[0] == '<') {
+		//this is a structural variant. Need to parse the tags to find the endpos.
+		_endPos = _startPos + fileReader->getVcfSVlen();
+	} else {
+		//endPos is just the startPos plus the length of the variant
+		_endPos = _startPos + _varAlt.size();
+	}
 	int2str(_endPos, _endPosStr);
-
 	fileReader->getField(2, _name);
-	fileReader->getField(4, _varRef);
 	fileReader->getField(5, _score);
 
 	return initOtherFieldsFromFile(fileReader);

test/merge/test-merge.sh

@@ -528,3 +528,17 @@ echo \
 $BT merge -i expFormat.bed > obs
 check exp obs
 rm obs exp
+
+
+###########################################################
+#  Test that struct vars in VCF get correct length
+###########################################################
+echo "    merge.t44...\c"
+echo \
+"19	252805	257416
+19	260364	261044
+19	265133	265691
+19	265985	266386" > exp
+$BT merge -i vcfSVtest.vcf > obs
+check exp obs
+rm obs exp

test/merge/vcfSVtest.vcf

+##fileformat=VCFv4.1
+19	252806	791255	G	<DEL>	70.90	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-389,-4611;END=253195;STR=+-:4;IMPRECISE;CIPOS=-2,137;CIEND=0,0;EVENT=791255;SUP=4;PESUP=4;SRSUP=0;EV=PE;PRIN;CSQ=intergenic_variant||||||||||
+19	260365	791256	C	<DEL>	33.71	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-680;END=261045;STR=+-:4;IMPRECISE;CIPOS=-1,257;CIEND=0,0;EVENT=791256;SUP=4;PESUP=4;SRSUP=0;EV=PE;PRIN;CSQ=upstream_gene_variant|||ENSG00000271846|CTD-3113P16.9|ENST00000607399|||||processed_pseudogene
+19	265134	791257	A	<DEL>	20.25	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-558;END=265692;STR=+-:4;IMPRECISE;CIPOS=-1,196;CIEND=0,0;EVENT=791257;SUP=4;PESUP=4;SRSUP=0;EV=PE;PRIN;CSQ=intergenic_variant||||||||||
+19	265986	791258	A	<DEL>	22.15	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-401;END=266387;STR=+-:6;IMPRECISE;CIPOS=-2,87;CIEND=0,0;EVENT=791258;SUP=6;PESUP=6;SRSUP=0;EV=PE;PRIN;CSQ=intergenic_variant||||||||||