ContextMerge::ContextMerge()
{
setSortedInput(true);
setUseMergedIntervals(true);
setColumnOpsMethods(true);
setExplicitBedOutput(true);
//merge has no default columnOps the way map does, so we'll need to clear those.
_keyListOps->setColumns("");
_keyListOps->setOperations("");
}
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);
}
ContextFisher::ContextFisher() {
setSortedInput(true);
setUseMergedIntervals(false);
}