Merge pull request #245 from nkindlon/master

Addressed >2 numbers in VCF SVLEN, can appear at endl w/ tab, semi-co…

src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp

@@ -139,6 +139,11 @@ bool SingleLineDelimTextFileReader::findDelimiters() {
 }
 
 int SingleLineDelimTextFileReader::getVcfSVlen() {
+
+	// The SVLEN field can appear anywhere in the info tag, and may be followed by a semi-colon, tab, newline, or end in NULL.
+	// it can contain one, two, or more numbers, which would be separated by a comma.
+	// We want the minimum number.
+
 	int startPos = _delimPositions[VCF_TAG_FIELD] +1;
 	const char *startPtr = strstr(_sLine.c_str() + startPos, "SVLEN=");
 	if (startPtr == NULL) {
@@ -146,16 +151,30 @@ int SingleLineDelimTextFileReader::getVcfSVlen() {
 		return 1;
 	}
 	startPtr +=6; // length of label "SVLEN="
-	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 = min(abs(num1), abs(num2));
-	} else {
-		endCoord = abs(str2chrPos(startPtr, endPtr - startPtr));
-	}
-	return endCoord;
+	const char *currPtr = startPtr;
+	const char *endPtr = _sLine.c_str() + _sLine.size();
+
+	int minVal = INT_MAX;
+	int currVal = 0;
+	QuickString currValStr;
+	while (1) {
+		if (currPtr == endPtr || *currPtr == ';' || *currPtr == '\t' || *currPtr == '\n' || *currPtr == ',') {
+			if (currPtr > startPtr) {
+				currValStr.assign(startPtr, currPtr - startPtr);
+				currVal = abs(str2chrPos(currValStr));
+				if (currVal < minVal) minVal = currVal;
+				startPtr = currPtr;
+			}
+
+			if (currPtr == endPtr || *currPtr != ',') {
+				//if end of line or non-comma delimiter, break.
+				break;
+			} else {
+				//skip the comma
+				startPtr++;
+			}
+		}
+		currPtr++;
+	};
+	return minVal;
 }

test/intersect/bug223_e.vcf

+##fileformat=VCFv4.1
+chr1	1	a	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||||||||||
+chr1	4	a	G	<DEL>	70.90	.	TOOL=LUMPY;SVTYPE=DEL;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||||||||||;SVLEN=-45,800,2	
\ No newline at end of file

test/intersect/bug223_f.vcf

+##fileformat=VCFv4.1
+chr1	1	a	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||||||||||
+chr1	4	a	G	<DEL>	70.90	.	TOOL=LUMPY;SVTYPE=DEL;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||||||||||;SVLEN=-10
\ No newline at end of file

test/intersect/test-intersect.sh

@@ -582,6 +582,49 @@ $BT intersect -a bug223_sv1_a.vcf -b bug223_sv1_b.vcf | cut -f1-6 > obs
 check exp obs
 rm exp obs
 
+##################################################################
+# see that SVLEN in VCF files can handle multiple numbers,
+# at end of line, followed by NULL.
+##################################################################
+echo "    intersect.t48...\c"
+echo \
+"chr1	1	a	G	<DEL>	70.90
+chr1	1	a	G	<DEL>	70.90
+chr1	4	a	G	<DEL>	70.90
+chr1	4	a	G	<DEL>	70.90" > exp
+$BT intersect -a bug223_d.vcf -b bug223_d.vcf | cut -f1-6 > obs
+check exp obs
+rm exp obs
+
+##################################################################
+# see that SVLEN in VCF files can handle multiple numbers,
+# at end of line, followed by a tab
+##################################################################
+echo "    intersect.t49...\c"
+echo \
+"chr1	1	a	G	<DEL>	70.90
+chr1	1	a	G	<DEL>	70.90
+chr1	4	a	G	<DEL>	70.90
+chr1	4	a	G	<DEL>	70.90" > exp
+$BT intersect -a bug223_e.vcf -b bug223_e.vcf | cut -f1-6 > obs
+check exp obs
+rm exp obs
+
+##################################################################
+# see that SVLEN in VCF files can handle single numbers,
+# at end of line, followed by null
+##################################################################
+echo "    intersect.t50...\c"
+echo \
+"chr1	1	a	G	<DEL>	70.90
+chr1	1	a	G	<DEL>	70.90
+chr1	4	a	G	<DEL>	70.90
+chr1	4	a	G	<DEL>	70.90" > exp
+$BT intersect -a bug223_f.vcf -b bug223_f.vcf | cut -f1-6 > obs
+check exp obs
+rm exp obs
+
+
 
 cd multi_intersect
 bash test-multi_intersect.sh