void ContextBase::testNameConventions(const Record *record) {
//Do nothing if using the -nonamecheck option,
//warning already given, or record is unmapped BAM record
if (getNameCheckDisabled() || _nameConventionWarningTripped || record->isUnmapped()) return;
int fileIdx = record->getFileIdx();
//
// First test whether chr in chrom names match
//
bool hasChr = record->hasChrInChromName();
testType testChrVal = fileHasChrInChromNames(fileIdx);
if (testChrVal == UNTESTED) {
_fileHasChrInChromNames[fileIdx] = hasChr ? YES : NO;
}
if ((_allFilesHaveChrInChromNames == YES && !hasChr) || (_allFilesHaveChrInChromNames == NO && hasChr)) {
nameConventionWarning(record, _fileNames[fileIdx], " has inconsistent naming convention for record:\n");
}
if (_allFilesHaveChrInChromNames == UNTESTED) {
_allFilesHaveChrInChromNames = hasChr ? YES : NO;
}
//
// Now test whether leading zero in chrom names match
//
bool zeroVal = record->hasLeadingZeroInChromName(hasChr);
testChrVal = fileHasLeadingZeroInChromNames(fileIdx);
if (testChrVal == UNTESTED) {
_fileHasLeadingZeroInChromNames[fileIdx] = zeroVal ? YES : NO;
}
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");
}
if (_allFileHaveLeadingZeroInChromNames == UNTESTED) {
_allFileHaveLeadingZeroInChromNames = zeroVal ? YES : NO;
}
}
bool ContextIntersect::isValidState()
{
if (!ContextBase::isValidState()) {
return false;
}
if (_queryFileIdx == -1 || _dbFileIdxs.size() == -0) {
_errorMsg = "\n***** ERROR: query and database files not specified. *****";
return false;
}
if (getAnyHit() && getNoHit()) {
_errorMsg = "\n***** ERROR: request either -u for anyHit OR -v for noHit, not both. *****";
return false;
}
if (getWriteCount()) {
if (getAnyHit()) {
_errorMsg = "\n***** ERROR: request either -c for writeCount OR -u for anyHit, not both. *****";
return false;
} else if (getWriteB()) {
_errorMsg = "\n***** ERROR: request either -c for writeCount OR -wb for writeB, not both. *****";
return false;
} else if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
_errorMsg = "\n***** ERROR: writeCount option is not valid with BAM query input, unless bed output is specified with -bed option. *****";
return false;
}
}
if (_haveFraction && (_overlapFraction <= 0.0 || _overlapFraction > 1.0)) {
_errorMsg = "\n***** ERROR: _overlapFraction must be in the range (0.0, 1.0]. *****";
return false;
}
if (getUseDBnameTags() && _dbNameTags.size() != _dbFileIdxs.size()) {
_errorMsg = "\n***** ERROR: Number of database name tags given does not match number of databases. *****";
return false;
}
if (getWriteOverlap()) {
if (getWriteA()) {
_errorMsg = "\n***** ERROR: request either -wa for writeA OR -wo for writeOverlap, not both. *****";
return false;
} else if (getWriteB()) {
_errorMsg = "\n***** ERROR: request either -wb for writeB OR -wo for writeOverlap, not both. *****";
return false;
} else if (getWriteCount()) {
_errorMsg = "\n***** ERROR: request either -c for writeCount OR -wo for writeOverlap, not both. *****";
return false;
} else if (getAnyHit()) {
_errorMsg = "\n***** ERROR: request either -u for anyHit OR -wo for writeOverlap, not both. *****";
return false;
} else if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
_errorMsg = "\n***** ERROR: writeAllOverlap option is not valid with BAM query input, unless bed output is specified with -bed option. *****";
return false;
}
}
if (getWriteB() || getLeftJoin()) {
if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
cerr << endl << "*****" << endl << "*****WARNING: -wb and -loj are ignored with bam input, unless bed output is specified with -bed option." << endl << "*****" << endl;
}
}
if (getSameStrand() && getDiffStrand()) {
_errorMsg = "\n***** ERROR: request -s for sameStrand, or -S for diffStrand, not both. *****";
return false;
}
if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && getPrintHeader()) {
cerr << endl << "*****" << endl << "*****WARNING: -header option is not valid for BAM input." << endl << "*****" << endl;
setPrintHeader(false);
}
if (getAnyHit() || getNoHit() || getWriteCount()) {
setPrintable(false);
}
if (_files.size() < 2 ) {
return false;
}
if (!getSortedInput() && getNameCheckDisabled()) {
_errorMsg = "\n***** ERROR: -nonamecheck option is only valid for sorted input. *****";
return false;
}
return true;
}
