Commit 3c14db01 authored by Neil Kindlon's avatar Neil Kindlon
Browse files

Corrected bug 218 by disabling intra-file name convention checking and...

Corrected bug 218 by disabling intra-file name convention checking and allowing -nonamecheck for unsorted files
parent 56c64385
......@@ -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");
}
......
......@@ -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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