Merge pull request #139 from nkindlon/master

fixes for bugs 100, 133, 136

src/utils/Contexts/ContextBase.cpp

@@ -32,7 +32,7 @@ ContextBase::ContextBase()
   _writeOverlap(false),
   _writeAllOverlap(false),
   _haveFraction(false),
-  _overlapFraction(1E-9),
+  _overlapFraction(0.0),
   _reciprocal(false),
   _sameStrand(false),
   _diffStrand(false),

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

@@ -13,6 +13,10 @@
 
 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();
 
@@ -24,6 +28,8 @@ 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;
@@ -38,6 +44,12 @@ 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/Record.cpp

@@ -160,15 +160,27 @@ bool Record::sameChromIntersects(const Record *record,
 	int otherStart = record->getStartPos();
 	int otherEnd = record->getEndPos();
 
+	bool otherZeroLen = (otherStart - otherEnd == 0);
 	int maxStart = max(_startPos, otherStart);
 	int minEnd = min(_endPos, otherEnd);
 
+	bool localZeroLen = (_endPos - _startPos == 0);
 	//rule out all cases of no intersection at all
 	if (minEnd < maxStart) {
 		return false;
 	}
 
 
+	if (overlapFraction == 0.0) {
+		//don't care about amount of overlap.
+		//however, if minEnd and maxStart are equal, and
+		//neither record is zeroLen, return false.
+		if (minEnd == maxStart && !otherZeroLen && !localZeroLen) {
+			return false;
+		}
+		return true;
+	}
+
 	int overlapBases = minEnd - maxStart;
 	int len = _endPos - _startPos;
 	int otherLen = otherEnd - otherStart;

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(3, _varAlt);
-	//endPos is just the startPos plus the length of the variant
-	_endPos = _startPos + _varAlt.size();
+	fileReader->getField(4, _varAlt);
+	fileReader->getField(3, _varRef);
+	if (_varAlt[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 + _varRef.size();
+	}
 	int2str(_endPos, _endPosStr);
-
 	fileReader->getField(2, _name);
-	fileReader->getField(4, _varRef);
 	fileReader->getField(5, _score);
 
 	return initOtherFieldsFromFile(fileReader);
@@ -33,8 +37,8 @@ bool VcfRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
 void VcfRecord::clear()
 {
 	BedPlusInterval::clear();
-	_varAlt.release();
 	_varRef.release();
+	_varAlt.release();
 }
 
 void VcfRecord::print(QuickString &outBuf) const {
@@ -70,10 +74,10 @@ void VcfRecord::printOtherFields(QuickString &outBuf) const {
 	outBuf.append('\t');
 	outBuf.append(_name);
 	outBuf.append('\t');
-	outBuf.append(_varAlt);
-	outBuf.append('\t');
 	outBuf.append(_varRef);
 	outBuf.append('\t');
+	outBuf.append(_varAlt);
+	outBuf.append('\t');
 	outBuf.append(_score);
 	for (int i= 0; i < (int)_otherIdxs.size(); i++) {
 		outBuf.append('\t');
@@ -98,10 +102,10 @@ const QuickString &VcfRecord::getField(int fieldNum) const
 	case 3:
 		return _name;
 	case 4:
-		return _varAlt;
+		return _varRef;
 		break;
 	case 5:
-		return _varRef;
+		return _varAlt;
 		break;
 	case 6:
 		return _score;

src/utils/FileRecordTools/Records/VcfRecord.h

@@ -32,8 +32,8 @@ public:
 	virtual const QuickString &getField(int fieldNum) const;
 
 protected:
-	QuickString _varAlt;
 	QuickString _varRef;
+	QuickString _varAlt;
 	void printOtherFields(QuickString &outBuf) const;
 };
 

src/utils/RecordOutputMgr/RecordOutputMgr.cpp

@@ -210,6 +210,7 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
 				if ((static_cast<ContextIntersect *>(_context))->getWriteAllOverlap()) {
 					// -wao the user wants to force the reporting of 0 overlap
 					if (printKeyAndTerminate(keyList)) {
+
 						_currBamBlockList = NULL;
 						return;
 					}
@@ -223,6 +224,7 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
 				else if ((static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
 					if (printKeyAndTerminate(keyList)) {
 						_currBamBlockList = NULL;
+
 						return;
 					}
 					tab();
@@ -230,11 +232,13 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
 					newline();
 					if (needsFlush()) flush();
 					_currBamBlockList = NULL;
+
 					return;
 				}
 			} else {
 				if (printBamRecord(keyList, true) == BAM_AS_BAM) {
 					_currBamBlockList = NULL;
+
 					return;
 				}
 				int hitIdx = 0;
@@ -252,14 +256,17 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
 			newline();
 		}
 		_currBamBlockList = NULL;
+
 		return;
 	} else if (_context->getProgram() == ContextBase::MAP) {
 		printKeyAndTerminate(keyList);
 		_currBamBlockList = NULL;
+
 		return;
 	} else if (_context->getProgram() == ContextBase::MERGE) {
 		printKeyAndTerminate(keyList);
 		_currBamBlockList = NULL;
+
 		return;
 	}
 }
@@ -380,6 +387,7 @@ void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record
 		newline();
 		if (needsFlush()) flush();
 	}
+	const_cast<Record *>(keyRecord)->adjustZeroLength();
 }
 
 void RecordOutputMgr::reportOverlapSummary(RecordKeyVector &keyList)

src/utils/general/ParseTools.cpp

@@ -2,6 +2,9 @@
 #include <climits>
 #include <cctype>
 #include <cstring>
+#include <cstdio>
+#include <cstdlib>
+#include <sstream>
 
 //This functions recognizes only numbers with digits, plus sign, minus sign, decimal point, e, or E. Hexadecimal and pointers not currently supported.
 bool isNumeric(const QuickString &str) {
@@ -19,12 +22,26 @@ int str2chrPos(const QuickString &str) {
 }
 
 int str2chrPos(const char *str, size_t ulen) {
+
 	if (ulen == 0) {
 		ulen = strlen(str);
 	}
+
+	//first test for exponents / scientific notation
+	bool hasExponent = false;
+	for (size_t i=0; i < ulen; i++) {
+		if (str[i] == 'e' || str[i] == 'E') {
+			std::istringstream ss(str);
+			double retVal;
+			ss >> retVal;
+			return (int)retVal;
+		}
+	}
+
 	int len=(int)ulen;
 	if (len < 1 || len > 10) {
-		return INT_MIN; //can't do more than 9 digits and a minus sign
+		fprintf(stderr, "***** ERROR: too many digits/characters for integer conversion in string %s. Exiting...\n", str);
+		exit(1);
 	}
 
 	register int sum=0;
@@ -39,9 +56,15 @@ int str2chrPos(const char *str, size_t ulen) {
 
 	for (int i=startPos; i < len; i++) {
 		char currChar = str[i];
+		if (currChar == 'e' || currChar == 'E') {
+			//default to atoi for scientific notation
+			return atoi(str);
+		}
 		if (!isdigit(currChar)) {
-			return INT_MIN;
+			fprintf(stderr, "***** ERROR: illegal character '%c' found in integer conversion of string %s. Exiting...\n", currChar, str);
+			exit(1);
 		}
+
 		int dig = currChar - 48; //ascii code for zero.
 		int power = len -i -1;
 
@@ -77,7 +100,7 @@ int str2chrPos(const char *str, size_t ulen) {
 			sum += dig *1000000000;
 			break;
 		default:
-			return INT_MIN;
+			return 0;
 			break;
 		}
 	}

test/intersect/a_testZeroLen.bed

+chr1	5	15	r1
+chr1	7	12	r3
+chr1	20	25	r2

test/intersect/a_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||||||||||

test/intersect/b_testZeroLen.bed

+chr1	9	9	m3
+chr1	50	150	m1
+chr2	20	25	m2

test/intersect/b_vcfSVtest.vcf

+##fileformat=VCFv4.1
+19	256900	791255	G	T	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	260800	791256	C	<INS>	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	265500	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	266003	791258	A	C	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||||||||||

test/intersect/new_test-intersect.sh

@@ -764,3 +764,53 @@ $BT intersect -a oneRecordNoNewline.bed -b oneRecordNoNewline.bed > obs
 check obs exp
 rm obs exp
 
+###########################################################
+#  Test zero length intersections in non-bam files.
+############################################################
+echo "    intersect.new.t65...\c"
+echo \
+"chr1	5	15	r1	chr1	9	9	m3	0
+chr1	7	12	r3	chr1	9	9	m3	0" > exp
+$BT intersect -a a_testZeroLen.bed -b b_testZeroLen.bed -wo > obs
+check exp obs
+rm exp obs
+
+###########################################################
+#  Test zero length intersections in non-bam files, -sorted
+############################################################
+echo "    intersect.new.t66...\c"
+echo \
+"chr1	5	15	r1	chr1	9	9	m3	0
+chr1	7	12	r3	chr1	9	9	m3	0" > exp
+$BT intersect -a a_testZeroLen.bed -b b_testZeroLen.bed -wo -sorted> obs
+check exp obs
+rm exp obs
+
+###########################################################
+#  Test vcf struct var intersection
+############################################################
+echo "    intersect.new.t67...\c"
+echo \
+"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	256900	791255	G	T	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	260800	791256	C	<INS>	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	265500	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||||||||||	19	265500	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||||||||||	19	266003	791258	A	C	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||||||||||" > exp
+$BT intersect -a a_vcfSVtest.vcf -b b_vcfSVtest.vcf -wa -wb >obs
+check exp obs
+rm exp obs
+
+###########################################################
+#  Test vcf struct var intersection, sorted
+############################################################
+echo "    intersect.new.t68...\c"
+echo \
+"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	256900	791255	G	T	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	260800	791256	C	<INS>	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	265500	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||||||||||	19	265500	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||||||||||	19	266003	791258	A	C	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||||||||||" > exp
+$BT intersect -a a_vcfSVtest.vcf -b b_vcfSVtest.vcf -wa -wb -sorted >obs
+check exp obs
+rm exp obs
+

test/merge/expFormat.bed

+chr1	8e02	830

test/merge/test-merge.sh

@@ -518,3 +518,27 @@ chr1	30	100" > exp
 $BT merge -i a.bed -iobuf 8192 > obs
 check exp obs
 rm exp obs
+
+###########################################################
+#  Test that scientific notation is allowed for coordinates
+###########################################################
+echo "    merge.t43...\c"
+echo \
+"chr1	800	830" > exp
+$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||||||||||