ContextBase::ContextBase()
:
_program(UNSPECIFIED_PROGRAM),
_allFilesOpened(false),
_genomeFile(NULL),
_outputFileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE),
_outputTypeDetermined(false),
_skipFirstArgs(0),
_showHelp(false),
_obeySplits(false),
_uncompressedBam(false),
_useBufferedOutput(true),
_ioBufSize(0),
_anyHit(false),
_noHit(false),
_writeA(false),
_writeB(false),
_leftJoin(false),
_writeCount(false),
_writeOverlap(false),
_writeAllOverlap(false),
_haveFraction(false),
_overlapFraction(1E-9),
_reciprocal(false),
_sameStrand(false),
_diffStrand(false),
_sortedInput(false),
_printHeader(false),
_printable(true),
_explicitBedOutput(false),
_queryFileIdx(-1),
_databaseFileIdx(-1),
_bamHeaderAndRefIdx(-1),
_maxNumDatabaseFields(0),
_useFullBamTags(false),
_reportCount(false),
_reportNames(false),
_reportScores(false),
_numOutputRecords(0),
_hasConstantSeed(false),
_seed(0),
_forwardOnly(false),
_reverseOnly(false),
_hasColumnOpsMethods(false),
_keyListOps(NULL),
_desiredStrand(FileRecordMergeMgr::ANY_STRAND),
_maxDistance(0),
_useMergedIntervals(false)
{
_programNames["intersect"] = INTERSECT;
_programNames["sample"] = SAMPLE;
_programNames["map"] = MAP;
_programNames["merge"] = MERGE;
if (hasColumnOpsMethods()) {
_keyListOps = new KeyListOps();
}
}
//for col ops, delimStr will appear between each item in
//a collapsed but delimited list.
bool ContextBase::handle_delim()
{
if (!hasColumnOpsMethods()) {
return false;
}
if ((_i+1) < _argc) {
_keyListOps->setDelimStr(_argv[_i + 1]);
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
}
return true;
}
//for col ops, delimStr will appear between each item in
//a collapsed but delimited list.
bool ContextBase::handle_delim()
{
if (!hasColumnOpsMethods()) {
_errorMsg = "\n***** ERROR: Can't set delimiter for tools without column operations. Exiting. *****";
return false;
}
if ((_i+1) < _argc) {
_keyListOps->setDelimStr(_argv[_i + 1]);
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
}
return true;
}
bool ContextBase::isValidState()
{
if (!openFiles()) {
return false;
}
if (!cmdArgsValid()) {
return false;
}
if (!determineOutputType()) {
return false;
}
if (_program != GROUP_BY &&
_files[0]->getRecordType() == FileRecordTypeChecker::NO_POS_PLUS_RECORD_TYPE)
{
_errorMsg = "ERROR: file ";
_errorMsg.append(_files[0]->getFileName());
_errorMsg.append(" has non positional records, which are only valid for \n");
_errorMsg.append(" the groupBy tool. Perhaps you are using a header");
_errorMsg.append(" line(s) that starts with \n");
_errorMsg.append(" something other than \"#\", \"chrom\", or \"chr\" (any case)?");
return false;
}
if (getObeySplits()) {
_splitBlockInfo = new BlockMgr(_overlapFractionA, _reciprocalFraction);
}
if (hasColumnOpsMethods()) {
if (hasIntersectMethods()) {
for (int i=0; i < (int)_dbFileIdxs.size(); i++) {
FileRecordMgr *dbFile = getFile(_dbFileIdxs[i]);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
} else {
FileRecordMgr *dbFile = getFile(0);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
//if user specified a precision, pass it to
//keyList ops
if (_reportPrecision != -1) {
_keyListOps->setPrecision(_reportPrecision);
}
}
return true;
}
ContextBase::~ContextBase()
{
delete _genomeFile;
_genomeFile = NULL;
//close all files and delete FRM objects.
for (int i=0; i < (int)_files.size(); i++) {
_files[i]->close();
delete _files[i];
_files[i] = NULL;
}
if (hasColumnOpsMethods()) {
delete _keyListOps;
_keyListOps = NULL;
}
}
bool ContextBase::handle_prec()
{
if (!hasColumnOpsMethods()) {
return false;
}
if ((_i+1) < _argc) {
int prec = atoi(_argv[_i + 1]);
if (prec < 1) {
_errorMsg += "\n***** ERROR: -prec must be followed by a positive integer. Exiting. *****";
return false;
}
_reportPrecision = prec;
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
_errorMsg += "\n***** ERROR: -prec must be followed by a positive integer. Exiting. *****";
return false;
}
bool ContextBase::isValidState()
{
if (!openFiles()) {
return false;
}
if (!cmdArgsValid()) {
return false;
}
if (!determineOutputType()) {
return false;
}
if (hasColumnOpsMethods()) {
FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
return true;
}
bool ContextBase::openFiles() {
//Make a vector of FileRecordMgr objects by going through the vector
//of filenames and opening each one.
if (_allFilesOpened) {
return true;
}
if (_fileNames.size() == 0) {
//No input was specified. Error and exit.
_errorMsg += "\n***** ERROR: No input file given. Exiting. *****";
return false;
}
_files.resize(_fileNames.size());
for (int i = 0; i < (int)_fileNames.size(); i++) {
FileRecordMgr *frm = getNewFRM(_fileNames[i], i);
if (hasGenomeFile()) {
frm->setGenomeFile(_genomeFile);
}
//If we're going to do column operations, and an input file
// is BAM, we'll need the full flags.
if (hasColumnOpsMethods()) {
setUseFullBamTags(true);
}
frm->setFullBamFlags(_useFullBamTags);
frm->setIsSorted(_sortedInput);
frm->setIoBufSize(_ioBufSize);
frm->setIsGroupBy(_program == GROUP_BY);
if (!frm->open(_inheader)) {
return false;
}
if (_noEnforceCoordSort) {
frm->setNoEnforceCoodSort(true);
}
_files[i] = frm;
}
_allFilesOpened = true;
return true;
}
ContextBase::~ContextBase()
{
delete _genomeFile;
_genomeFile = NULL;
delete _splitBlockInfo;
_splitBlockInfo = NULL;
if (_nameConventionWarningTripped) {
cerr << _nameConventionWarningMsg << endl;
}
//close all files and delete FRM objects.
for (int i=0; i < (int)_files.size(); i++) {
_files[i]->close();
delete _files[i];
_files[i] = NULL;
}
if (hasColumnOpsMethods()) {
delete _keyListOps;
_keyListOps = NULL;
}
}
bool ContextBase::isValidState()
{
if (!openFiles()) {
return false;
}
if (!cmdArgsValid()) {
return false;
}
if (!determineOutputType()) {
return false;
}
if (getObeySplits()) {
_splitBlockInfo = new BlockMgr(_overlapFraction, _reciprocal);
}
if (hasColumnOpsMethods()) {
if (hasIntersectMethods()) {
for (int i=0; i < (int)_dbFileIdxs.size(); i++) {
FileRecordMgr *dbFile = getFile(_dbFileIdxs[i]);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
} else {
FileRecordMgr *dbFile = getFile(0);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
//if user specified a precision, pass it to
//keyList ops
if (_reportPrecision != -1) {
_keyListOps->setPrecision(_reportPrecision);
}
}
return true;
}
bool ContextFisher::isValidState()
{
if (!ContextIntersect::isValidState()) {
return false;
}
// Tests for stranded merge
//
if (_desiredStrand != FileRecordMergeMgr::ANY_STRAND) { // requested stranded merge
for (int i=0; i < getNumInputFiles(); i++) {
// make sure file has strand.
if (!getFile(i)->recordsHaveStrand()) {
_errorMsg = "\n***** ERROR: stranded merge requested, but input file ";
_errorMsg += getInputFileName(i);
_errorMsg += " does not have strands. *****";
return false;
}
//make sure file is not VCF.
if (getFile(1)->getFileType() == FileRecordTypeChecker::VCF_FILE_TYPE) {
_errorMsg = "\n***** ERROR: stranded merge not supported for VCF file ";
_errorMsg += getInputFileName(i);
_errorMsg += ". *****";
return false;
}
}
}
if (_genomeFile == NULL){
_errorMsg = "\nERROR*****: specify -g genome file*****\n";
return false;
}
//column operations not allowed with BAM input
if (hasColumnOpsMethods() &&
getFile(0)->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
_errorMsg = "\n***** ERROR: stranded merge not supported for VCF files. *****";
return false;
}
return true;
}
const string &ContextBase::getColumnOpsVal(RecordKeyVector &keyList) const {
if (!hasColumnOpsMethods()) {
return _nullStr;
}
return _keyListOps->getOpVals(keyList);
}
ContextBase::ContextBase()
:
_program(UNSPECIFIED_PROGRAM),
_files(NULL),
_allFilesOpened(false),
_genomeFile(NULL),
_outputFileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE),
_outputTypeDetermined(false),
_skipFirstArgs(0),
_showHelp(false),
_obeySplits(false),
_uncompressedBam(false),
_useBufferedOutput(true),
_ioBufSize(0),
_anyHit(false),
_noHit(false),
_writeA(false),
_writeB(false),
_leftJoin(false),
_writeCount(false),
_writeOverlap(false),
_writeAllOverlap(false),
_haveFractionA(false),
_haveFractionB(false),
_overlapFractionA(0.0),
_overlapFractionB(0.0),
_reciprocalFraction(false),
_eitherFraction(false),
_sameStrand(false),
_diffStrand(false),
_sortedInput(false),
_sortOutput(false),
_reportDBnameTags(false),
_reportDBfileNames(false),
_printHeader(false),
_printable(true),
_explicitBedOutput(false),
_queryFileIdx(-1),
_bamHeaderAndRefIdx(-1),
_maxNumDatabaseFields(0),
_useFullBamTags(false),
_numOutputRecords(0),
_hasConstantSeed(false),
_seed(0),
_forwardOnly(false),
_reverseOnly(false),
_nameCheckDisabled(false),
_hasColumnOpsMethods(false),
_keyListOps(NULL),
_desiredStrand(FileRecordMergeMgr::ANY_STRAND),
_maxDistance(0),
_useMergedIntervals(false),
_reportPrecision(-1),
_splitBlockInfo(NULL),
_allFilesHaveChrInChromNames(UNTESTED),
_allFileHaveLeadingZeroInChromNames(UNTESTED),
_noEnforceCoordSort(false),
_inheader(false),
_nameConventionWarningTripped(false)
{
_programNames["intersect"] = INTERSECT;
_programNames["sample"] = SAMPLE;
_programNames["map"] = MAP;
_programNames["merge"] = MERGE;
_programNames["closest"] = CLOSEST;
_programNames["subtract"] = SUBTRACT;
_programNames["jaccard"] = JACCARD;
_programNames["spacing"] = SPACING;
_programNames["fisher"] = FISHER;
_programNames["sample"] = SAMPLE;
_programNames["coverage"] = COVERAGE;
_programNames["complement"] = COMPLEMENT;
_programNames["groupby"] = GROUP_BY;
if (hasColumnOpsMethods()) {
_keyListOps = new KeyListOps();
}
}
