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R3
legacy
bedtools2
Commits
488b0593
Commit
488b0593
authored
Mar 11, 2015
by
Neil Kindlon
Browse files
Addressed bug #208; seg fault when VCF doesn't have SVLEN for imprecise variants.
parent
509e6fee
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
View file @
488b0593
...
...
@@ -140,7 +140,11 @@ bool SingleLineDelimTextFileReader::findDelimiters() {
int
SingleLineDelimTextFileReader
::
getVcfSVlen
()
{
int
startPos
=
_delimPositions
[
VCF_TAG_FIELD
]
+
1
;
const
char
*
startPtr
=
strstr
(
_sLine
.
c_str
()
+
startPos
,
"SVLEN="
)
+
6
;
const
char
*
startPtr
=
strstr
(
_sLine
.
c_str
()
+
startPos
,
"SVLEN="
);
if
(
startPtr
==
NULL
)
{
cerr
<<
"WARNING: line number "
<<
_lineNum
<<
" of file "
<<
_filename
<<
" has an imprecise variant, but no SVLEN specified. Defaulting to length 1."
<<
endl
;
return
1
;
}
const
char
*
endPtr
=
strchr
(
startPtr
,
';'
);
const
char
*
midPtr
=
strchr
(
startPtr
,
','
);
int
endCoord
=
-
1
;
...
...
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