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hub / github.com/arq5x/bedtools2 / KeyListOpsHelp

Function KeyListOpsHelp

src/utils/KeyListOps/KeyListOps.cpp:344–381  ·  view source on GitHub ↗

Source from the content-addressed store, hash-verified

342}
343
344void KeyListOpsHelp() {
345
346 cerr << "\t-c\t" << "Specify columns from the B file to map onto intervals in A." << endl;
347 cerr << "\t\tDefault: 5." << endl;
348 cerr << "\t\tMultiple columns can be specified in a comma-delimited list." << endl << endl;
349
350 cerr << "\t-o\t" << "Specify the operation that should be applied to -c." << endl;
351 cerr << "\t\tValid operations:" << endl;
352 cerr << "\t\t sum, min, max, absmin, absmax," << endl;
353 cerr << "\t\t mean, median, mode, antimode" << endl;
354 cerr << "\t\t stdev, sstdev" << endl;
355 cerr << "\t\t collapse (i.e., print a delimited list (duplicates allowed)), " << endl;
356 cerr << "\t\t distinct (i.e., print a delimited list (NO duplicates allowed)), " << endl;
357 cerr << "\t\t distinct_sort_num (as distinct, sorted numerically, ascending)," << endl;
358 cerr << "\t\t distinct_sort_num_desc (as distinct, sorted numerically, desscending)," << endl;
359 cerr << "\t\t distinct_only (delimited list of only unique values)," << endl;
360 cerr << "\t\t count" << endl;
361 cerr << "\t\t count_distinct (i.e., a count of the unique values in the column), " << endl;
362 cerr << "\t\t first (i.e., just the first value in the column), " << endl;
363 cerr << "\t\t last (i.e., just the last value in the column), " << endl;
364 cerr << "\t\tDefault: sum" << endl;
365 cerr << "\t\tMultiple operations can be specified in a comma-delimited list." << endl << endl;
366
367 cerr << "\t\tIf there is only column, but multiple operations, all operations will be" << endl;
368 cerr << "\t\tapplied on that column. Likewise, if there is only one operation, but" << endl;
369 cerr << "\t\tmultiple columns, that operation will be applied to all columns." << endl;
370 cerr << "\t\tOtherwise, the number of columns must match the the number of operations," << endl;
371 cerr << "\t\tand will be applied in respective order." << endl;
372 cerr << "\t\tE.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5," << endl;
373 cerr << "\t\tthe mean of column 4, and the count of column 6." << endl;
374 cerr << "\t\tThe order of output columns will match the ordering given in the command." << endl << endl<<endl;
375
376 cerr << "\t-delim\t" << "Specify a custom delimiter for the collapse operations." << endl;
377 cerr << "\t\t- Example: -delim \"|\"" << endl;
378 cerr << "\t\t- Default: \",\"." << endl << endl;
379
380 cerr << "\t-prec\t" << "Sets the decimal precision for output (Default: 5)" << endl << endl;
381}

Callers 2

map_helpFunction · 0.85
merge_helpFunction · 0.85

Calls

no outgoing calls

Tested by

no test coverage detected