From 2f55cedaff867340a18dfe012009f3ded28f1e88 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 13 Feb 2012 19:52:10 -0500
Subject: [PATCH] tweaks to help menus
---
src/flankBed/flankBedMain.cpp | 7 +++++--
src/pairToPair/pairToPairMain.cpp | 4 ++--
2 files changed, 7 insertions(+), 4 deletions(-)
diff --git a/src/flankBed/flankBedMain.cpp b/src/flankBed/flankBedMain.cpp
index 311eaee5..6a15a04b 100644
--- a/src/flankBed/flankBedMain.cpp
+++ b/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;
diff --git a/src/pairToPair/pairToPairMain.cpp b/src/pairToPair/pairToPairMain.cpp
index a778db25..81fdee8b 100644
--- a/src/pairToPair/pairToPairMain.cpp
+++ b/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;
--
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