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R3
legacy
bedtools2
Commits
7553f4a1
Commit
7553f4a1
authored
Apr 20, 2015
by
Aaron Quinlan
Browse files
Merge pull request #222 from nkindlon/master
Corrected bug 218 by disabling intra-file name convention checking and a...
parents
43f88db6
3c14db01
Changes
2
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Inline
Side-by-side
src/utils/Contexts/ContextBase.cpp
View file @
7553f4a1
...
...
@@ -646,9 +646,10 @@ void ContextBase::testNameConventions(const Record *record) {
if
(
testChrVal
==
UNTESTED
)
{
_fileHasChrInChromNames
[
fileIdx
]
=
hasChr
?
YES
:
NO
;
}
else
if
((
testChrVal
==
YES
&&
!
hasChr
)
||
(
testChrVal
==
NO
&&
hasChr
))
{
nameConventionWarning
(
record
,
_fileNames
[
fileIdx
],
" has inconsistent naming convention for record:
\n
"
);
}
// else if ((testChrVal == YES && !hasChr) || (testChrVal == NO && hasChr)) {
// nameConventionWarning(record, _fileNames[fileIdx], " has inconsistent naming convention for record:\n");
// }
if
((
_allFilesHaveChrInChromNames
==
YES
&&
!
hasChr
)
||
(
_allFilesHaveChrInChromNames
==
NO
&&
hasChr
))
{
nameConventionWarning
(
record
,
_fileNames
[
fileIdx
],
" has a record where naming convention is inconsistent with other files:
\n
"
);
}
...
...
@@ -667,9 +668,10 @@ void ContextBase::testNameConventions(const Record *record) {
testChrVal
=
fileHasLeadingZeroInChromNames
(
fileIdx
);
if
(
testChrVal
==
UNTESTED
)
{
_fileHasLeadingZeroInChromNames
[
fileIdx
]
=
zeroVal
?
YES
:
NO
;
}
else
if
((
testChrVal
==
YES
&&
!
zeroVal
)
||
(
testChrVal
==
NO
&&
zeroVal
))
{
nameConventionWarning
(
record
,
_fileNames
[
fileIdx
],
" has inconsistent naming convention (leading zero) for record:
\n
"
);
}
// else if ((testChrVal == YES && !zeroVal) || (testChrVal == NO && zeroVal)) {
// nameConventionWarning(record, _fileNames[fileIdx], " has inconsistent naming convention (leading zero) for record:\n");
// }
if
((
_allFileHaveLeadingZeroInChromNames
==
YES
&&
!
zeroVal
)
||
(
_allFileHaveLeadingZeroInChromNames
==
NO
&&
zeroVal
))
{
nameConventionWarning
(
record
,
_fileNames
[
fileIdx
],
" has a record where naming convention (leading zero) is inconsistent with other files:
\n
"
);
}
...
...
src/utils/Contexts/ContextIntersect.cpp
View file @
7553f4a1
...
...
@@ -168,10 +168,6 @@ bool ContextIntersect::isValidState()
if
(
_files
.
size
()
<
2
)
{
return
false
;
}
if
(
!
getSortedInput
()
&&
getNameCheckDisabled
())
{
_errorMsg
=
"
\n
***** ERROR: -nonamecheck option is only valid for sorted input. *****"
;
return
false
;
}
return
true
;
}
...
...
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