bool ContextBase::handle_i()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -i option given, but no input file specified. *****";
return false;
}
addInputFile(_argv[_i+1]);
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextBase::handle_n()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -n option given, but no number of output records specified. *****";
return false;
}
setNumOutputRecords(atoi(_argv[_i + 1]));
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextGroupBy::handle_g()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -g option given, but columns to group not specified. *****";
return false;
}
_groupStr = _argv[_i+1];
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextBase::handle_g()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -g option given, but no genome file specified. *****";
return false;
}
openGenomeFile(_argv[_i+1]);
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextIntersect::handle_abam()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -abam option given, but no query BAM file specified. *****";
return false;
}
addInputFile(_argv[_i+1]);
_queryFileIdx = getNumInputFiles() -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()) {
return false;
}
if ((_i+1) < _argc) {
_keyListOps->setDelimStr(_argv[_i + 1]);
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
}
return true;
}
bool ContextBase::handle_seed()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -seed option given, but no seed specified. *****";
return false;
}
_hasConstantSeed = true;
_seed = atoi(_argv[_i+1]);
srand(_seed);
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 ContextMerge::handle_d() {
if ((_i+1) < _argc) {
if (isNumeric(_argv[_i+1])) {
int dist = str2chrPos(_argv[_i+1]);
_maxDistance = dist;
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
}
_errorMsg = "\n***** ERROR: -d option must be followed by an integer value *****";
return false;
}
bool ContextFisher::handle_exclude()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -exclude option given, but no file specified. *****";
return false;
}
do {
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
} while (_argc > _i+1 && _argv[_i+1][0] != '-');
setExcludeFile(string(_argv[_i]));
return true;
}
bool ContextMerge::handle_nms()
{
markUsed(_i - _skipFirstArgs);
_errorMsg = "\n***** ERROR: -nms option is deprecated. Please see the documentation for the -c and -o column operation options. *****";
return false;
}
bool ContextIntersect::handle_wao()
{
setWriteAllOverlap(true);
setWriteOverlap(true);
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextIntersect::handle_names()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -b option given, but no database names specified. *****";
return false;
}
do {
addDatabaseNameTag(_argv[_i+1]);
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
} while (_argc > _i+1 && _argv[_i+1][0] != '-');
setUseDBnameTags(true);
return true;
}
bool ContextMerge::handle_scores()
{
// No longer supporting this deprecated option.
markUsed(_i - _skipFirstArgs);
_errorMsg = "\n***** ERROR: -scores option is deprecated. Please see the documentation for the -c and -o column operation options. *****";
return false;
}
bool ContextIntersect::handle_b()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -b option given, but no database file specified. *****";
return false;
}
do {
addInputFile(_argv[_i+1]);
int fileId = getNumInputFiles() -1;
_dbFileIdxs.push_back(fileId);
_fileIdsToDbIdxs[fileId] = _dbFileIdxs.size() -1;
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
} while (_argc > _i+1 && _argv[_i+1][0] != '-');
return true;
}
bool ContextSample::handle_s()
{
_sameStrand = true;
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -s option given, but \"forward\" or \"reverse\" not specified. *****";
return false;
}
if (strcmp(_argv[_i+1], "forward") == 0) {
_forwardOnly = true;
} else if (strcmp(_argv[_i+1], "reverse") == 0) {
_reverseOnly = true;
} else {
_errorMsg = "\n***** ERROR: -s option given, but \"forward\" or \"reverse\" not specified. *****";
return false;
}
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextMerge::handle_S() {
if ((_i+1) < _argc) {
bool validChar = false;
if (_argv[_i+1][0] == '+') {
_desiredStrand = FileRecordMergeMgr::SAME_STRAND_FORWARD;
validChar = true;
} else if (_argv[_i+1][0] == '-') {
validChar = true;
_desiredStrand = FileRecordMergeMgr::SAME_STRAND_REVERSE;
}
if (validChar) {
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
}
_errorMsg = "\n***** ERROR: -S option must be followed by + or -. *****";
return false;
}
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;
}
void Topic::addSubscription(Subscription &subscription)
{
_readWriteLock.lockForWrite();
markUsed();
_subscriptions.append(&subscription);
if(_state == NO_SUBSCRIPTIONS_STATE)
_state = HAS_SUBSCRIPTIONS_STATE;
else
_state = NO_SUBSCRIPTIONS_STATE;
_readWriteLock.unlock();
}
bool ContextClosest::handle_mdb()
{
bool mdbError = false;
if ((_i+1) < _argc) {
QuickString mdbStr(_argv[_i+1]);
if (mdbStr == "each") {
_multiDbMode = EACH_DB;
} else if (mdbStr == "all") {
_multiDbMode = ALL_DBS;
} else {
mdbError = true;
}
} else {
mdbError = true;
}
if (!mdbError) {
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
_errorMsg = "*****ERROR: Request \"each\" or \"last\" for Multiple Database Mode (-mdb)";
return false;
}
void Topic::removeSubscription(Subscription &subscription)
{
_readWriteLock.lockForWrite();
markUsed();
_subscriptions.removeOne(&subscription);
if(_subscriptions.count() == 0)
{
if(_state == HAS_SUBSCRIPTIONS_STATE)
_state = NO_SUBSCRIPTIONS_STATE;
else
_state = HAS_SUBSCRIPTIONS_STATE;
}
_readWriteLock.unlock();
}
bool ContextFisher::parseCmdArgs(int argc, char **argv, int skipFirstArgs)
{
_argc = argc;
_argv = argv;
_skipFirstArgs = skipFirstArgs;
if (_argc < 2) {
setShowHelp(true);
return false;
}
setProgram(_programNames[argv[0]]);
_argsProcessed.resize(_argc - _skipFirstArgs, false);
for (_i=_skipFirstArgs; _i < argc; _i++) {
if (isUsed(_i - _skipFirstArgs)) {
continue;
}
else if (strcmp(_argv[_i], "-s") == 0) {
if (!handle_s()) return false;
}
else if (strcmp(_argv[_i], "-S") == 0) {
if (!handle_S()) return false;
}
else if (strcmp(_argv[_i], "-exclude") == 0) {
if (!handle_exclude()) return false;
}
if (strcmp(_argv[_i], "-g") == 0) {
if (!handle_g()) return false;
}
if(strcmp(_argv[_i], "-m") == 0) {
markUsed(_i - _skipFirstArgs);
setUseMergedIntervals(true);
}
}
return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
}
bool ContextBase::handle_split()
{
setObeySplits(true);
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextSubtract::handle_N() {
_removeSum = true;
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextBase::handle_nonamecheck()
{
setNameCheckDisabled(true);
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextBase::handle_sortout()
{
setSortOutput(true);
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextBase::handle_ubam()
{
setUncompressedBam(true);
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextBase::handle_h()
{
setShowHelp(true);
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextBase::handle_nobuf()
{
setUseBufferedOutput(false);
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextBase::handle_header()
{
setPrintHeader(true);
markUsed(_i - _skipFirstArgs);
return true;
}
