Commit 5f0362f8 authored by Neil Kindlon's avatar Neil Kindlon
Browse files

Changed common help to remove -names, -filenames, and -sortout from all tools...

Changed common help to remove -names, -filenames, and -sortout from all tools but intersect and closest.
parent 8edf2662
...@@ -73,6 +73,7 @@ void closest_help(void) { ...@@ -73,6 +73,7 @@ void closest_help(void) {
cerr << "\t\tFor BED, the 4th column is compared." << endl << endl; cerr << "\t\tFor BED, the 4th column is compared." << endl << endl;
IntersectCommonHelp(); IntersectCommonHelp();
multiDbOutputHelp();
allToolsCommonHelp(); allToolsCommonHelp();
cerr << "Notes: " << endl; cerr << "Notes: " << endl;
......
...@@ -33,6 +33,7 @@ void intersect_help(void) { ...@@ -33,6 +33,7 @@ void intersect_help(void) {
IntersectCommonHelp(); IntersectCommonHelp();
sortedHelp(); sortedHelp();
multiDbOutputHelp();
allToolsCommonHelp(); allToolsCommonHelp();
cerr << "Notes: " << endl; cerr << "Notes: " << endl;
......
...@@ -69,7 +69,12 @@ void IntersectCommonHelp() { ...@@ -69,7 +69,12 @@ void IntersectCommonHelp() {
cerr << "\t-g\t" << "Provide a genome file to enforce consistent chromosome sort order" << endl; cerr << "\t-g\t" << "Provide a genome file to enforce consistent chromosome sort order" << endl;
cerr <<"\t\tacross input files. Only applies when used with -sorted option." << endl << endl; cerr <<"\t\tacross input files. Only applies when used with -sorted option." << endl << endl;
cerr << "\t-nonamecheck\t" << "For sorted data, don't throw an error if the file has different naming conventions" << endl;
cerr << "\t\t\tfor the same chromosome. ex. \"chr1\" vs \"chr01\"." << endl << endl;
}
void multiDbOutputHelp() {
cerr << "\t-names\t" << "When using multiple databases, provide an alias for each that" << endl; cerr << "\t-names\t" << "When using multiple databases, provide an alias for each that" << endl;
cerr <<"\t\twill appear instead of a fileId when also printing the DB record." << endl << endl; cerr <<"\t\twill appear instead of a fileId when also printing the DB record." << endl << endl;
...@@ -78,10 +83,6 @@ void IntersectCommonHelp() { ...@@ -78,10 +83,6 @@ void IntersectCommonHelp() {
cerr << "\t-sortout\t" << "When using multiple databases, sort the output DB hits" << endl; cerr << "\t-sortout\t" << "When using multiple databases, sort the output DB hits" << endl;
cerr << "\t\t\tfor each record." << endl << endl; cerr << "\t\t\tfor each record." << endl << endl;
cerr << "\t-nonamecheck\t" << "For sorted data, don't throw an error if the file has different naming conventions" << endl;
cerr << "\t\t\tfor the same chromosome. ex. \"chr1\" vs \"chr01\"." << endl << endl;
} }
......
...@@ -18,5 +18,6 @@ extern void allToolsCommonHelp(); ...@@ -18,5 +18,6 @@ extern void allToolsCommonHelp();
extern void IntersectCommonHelp(); extern void IntersectCommonHelp();
extern void IntersectOutputHelp(); extern void IntersectOutputHelp();
extern void sortedHelp(); extern void sortedHelp();
extern void multiDbOutputHelp();
#endif /* COMMONHELPFILE_H_ */ #endif /* COMMONHELPFILE_H_ */
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