bool ContextMap::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;
}
if (strcmp(_argv[_i], "-c") == 0) {
//bypass intersect's use of the -c option, because -c
//means writeCount for intersect, but means columns for map.
if (!ContextBase::handle_c()) return false;
}
}
return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
}
bool ContextMap::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], "-o") == 0) {
if (!handle_o()) return false;
}
else if (strcmp(_argv[_i], "-c") == 0) {
if (!handle_c()) return false;
}
else if (strcmp(_argv[_i], "-null") == 0) {
if (!handle_null()) return false;
}
}
return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
}
bool ContextBase::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;
}
if (strcmp(_argv[_i], "-i") == 0) {
if (!handle_i()) return false;
}
else if (strcmp(_argv[_i], "-g") == 0) {
if (!handle_g()) return false;
}
else if ((strcmp(_argv[_i], "-h") == 0) || (strcmp(_argv[_i], "--help") == 0)) {
if (!handle_h()) return false;
}
else if (strcmp(_argv[_i], "-split") == 0) {
if (!handle_split()) return false;
}
else if (strcmp(_argv[_i], "-bed") == 0) {
if (!handle_bed()) return false;
}
else if (strcmp(_argv[_i], "-ubam") == 0) {
if (!handle_ubam()) return false;
}
else if (strcmp(_argv[_i], "-fbam") == 0) {
if (!handle_fbam()) return false;
}
else if(strcmp(_argv[_i], "-sorted") == 0) {
if (!handle_sorted()) return false;
}
else if (strcmp(_argv[_i], "-nobuf") == 0) {
if (!handle_nobuf()) return false;
}
else if (strcmp(_argv[_i], "-header") == 0) {
if (!handle_header()) return false;
}
else if (strcmp(_argv[_i], "-n") == 0) {
if (!handle_n()) return false;
}
else if (strcmp(_argv[_i], "-seed") == 0) {
if (!handle_seed()) return false;
}
}
return true;
}
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_h()
{
setShowHelp(true);
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextIntersect::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;
}
if (strcmp(_argv[_i], "-a") == 0) {
if (!handle_a()) return false;
}
else if (strcmp(_argv[_i], "-abam") == 0) {
if (!handle_abam()) return false;
}
else if (strcmp(_argv[_i], "-b") == 0) {
if (!handle_b()) return false;
}
else if (strcmp(_argv[_i], "-names") == 0) {
if (!handle_names()) return false;
}
else if (strcmp(_argv[_i], "-filenames") == 0) {
if (!handle_filenames()) return false;
}
else if (strcmp(_argv[_i], "-u") == 0) {
if (!handle_u()) return false;
}
else if (strcmp(_argv[_i], "-f") == 0) {
if (!handle_f()) return false;
}
else if (strcmp(_argv[_i], "-wa") == 0) {
if (!handle_wa()) return false;
}
else if (strcmp(_argv[_i], "-wao") == 0) {
if (!handle_wao()) return false;
}
else if (strcmp(_argv[_i], "-wb") == 0) {
if (!handle_wb()) return false;
}
else if (strcmp(_argv[_i], "-wo") == 0) {
if (!handle_wo()) return false;
}
else if (strcmp(_argv[_i], "-c") == 0) {
if (!handle_c()) return false;
}
else if(strcmp(_argv[_i], "-r") == 0) {
if (!handle_r()) return false;
}
else if (strcmp(_argv[_i], "-v") == 0) {
if (!handle_v()) return false;
}
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], "-loj") == 0) {
if (!handle_loj()) return false;
}
}
return ContextBase::parseCmdArgs(argc, argv, _skipFirstArgs);
}
