Commit fe6b3098 authored by Aaron Quinlan's avatar Aaron Quinlan
Browse files

Merge pull request #7 from nkindlon/master

Added -nobuf option and definition to intersect help menu.
parents 465f72d8 b2f01dc8
......@@ -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;
......
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