diff --git a/src/intersectFile/intersectMain.cpp b/src/intersectFile/intersectMain.cpp index 4aac270a30a377b74b6e09fa47fd5d3189361820..0e032f94bd3695a00ed88ab97d5f2e48434f6dd8 100644 --- a/src/intersectFile/intersectMain.cpp +++ b/src/intersectFile/intersectMain.cpp @@ -110,7 +110,15 @@ void intersect_help(void) { cerr <<"\t\tacross input files. Only applies when used with -sorted option." << endl << endl; cerr << "\t-header\t" << "Print the header from the A file prior to results." << endl << endl; - + + cerr << "\t-nobuf\t" << "Disable buffered output. Using this option will cause each line"<< endl; + cerr <<"\t\tof output to be printed as it is generated, rather than saved" << endl; + cerr <<"\t\tin a buffer. This will make printing large output files " << endl; + + cerr <<"\t\tnoticeably slower, but can be useful in conjunction with" << endl; + cerr <<"\t\tother software tools and scripts that need to process one" << endl; + cerr <<"\t\tline of bedtools output at a time." << endl << endl; + cerr << "Notes: " << endl; cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl; cerr << "\tand exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not" << endl;