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Fix issue #832 #847

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Fix issue #832 #847

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2 changes: 1 addition & 1 deletion src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -187,5 +187,5 @@ CHRPOS SingleLineDelimTextFileReader::getVcfSVlen() {
}
}
// not found
return INT_MIN;
return 1;
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As long as other place in bedtools doesn't handles negative length (which means returning INT_MIN would only causing interger overflow which cause unpredictable bugs rather than anything we expected), I believe return INT_MIN doesn't make sense anyway. Alternatively, we can turn this into an error, but I am not sure if this is actually valid VCF

}
4 changes: 3 additions & 1 deletion src/utils/FileRecordTools/Records/VcfRecord.cpp
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Expand Up @@ -23,7 +23,9 @@ bool VcfRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
if (_varAlt[0] == '<') {
// this is a structural variant. Need to parse the tags to find the endpos,
// UNLESS it's an insertion.
if (!(_varAlt[1] == 'I' && _varAlt[2] == 'N' && _varAlt[3] == 'S')) {
if (memcmp(_varAlt.c_str(), "<*>", 3) == 0) {
_endPos = _startPos + 1;
} else if (memcmp(_varAlt.c_str(), "<INS>", 5) != 0) {
_endPos = _startPos + fileReader->getVcfSVlen();
} else {
//for insertions, treat as zero-length records
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