tweaks to help menus

src/flankBed/flankBedMain.cpp

@@ -151,7 +151,7 @@ void flank_help(void) {
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome> [-b <int> or (-l and -r)]" << endl << endl;
 
     cerr << "Options: " << endl;
-    cerr << "\t-b\t"                << "Create flanking intervak using -b base pairs in each direction." << endl;
+    cerr << "\t-b\t"                << "Create flanking interval(s) using -b base pairs in each direction." << endl;
     cerr                            << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl;
 
     cerr << "\t-l\t"                << "The number of base pairs that a flank should start from" << endl;
@@ -176,8 +176,11 @@ void flank_help(void) {
     cerr << "\t(1)  Starts will be set to 0 if options would force it below 0." << endl;
     cerr << "\t(2)  Ends will be set to the chromosome length if requested flank would" << endl;
     cerr <<        "\tforce it above the max chrom length." << endl;
+    cerr << "\t(3)  In contrast to slop, which _extends_ intervals, bedtools flank" << endl;
+    cerr <<        "\tcreates new intervals from the regions just up- and down-stream" << endl;
+    cerr <<        "\tof your existing intervals." << endl;
 
-    cerr << "\t(3)  The genome file should tab delimited and structured as follows:" << endl;
+    cerr << "\t(4)  The genome file should tab delimited and structured as follows:" << endl;
     cerr << "\n\t<chromName><TAB><chromSize>" << endl << endl;
     cerr << "\tFor example, Human (hg19):" << endl;
     cerr << "\tchr1\t249250621" << endl;

src/pairToPair/pairToPairMain.cpp

@@ -163,12 +163,12 @@ void pairtopair_help(void) {
     cerr                                << "\t\teither\tReport overlaps if either ends of A overlap B." << endl;
     cerr                                << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
     cerr                                << "\t\tnotboth\tReport overlaps if one or neither of A's overlap B." << endl;
-    
     cerr                                << "\t\t- Default = both." << endl << endl;
 
-    cerr << "\t-slop \t"                << "The amount of slop (in b.p.). to be added to each footprint." << endl;
+    cerr << "\t-slop \t"                << "The amount of slop (in b.p.). to be added to each footprint of A." << endl;
     cerr                                << "\t\t*Note*: Slop is subtracted from start1 and start2" << endl;
     cerr                                << "\t\t\tand added to end1 and end2." << endl << endl;
+    cerr                                << "\t\t- Default = 0." << endl << endl;
     
     cerr << "\t-ss\t"                   << "Add slop based to each BEDPE footprint based on strand." << endl;
     cerr                                << "\t\t- If strand is \"+\", slop is only added to the end coordinates." << endl;