From da8bf325cedc927290373a17fb0f19f79f55beea Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 29 Jun 2011 16:27:44 -0400
Subject: [PATCH] Updated help messages
---
src/multiBamCov/multiBamCovMain.cpp | 5 +++--
src/tagBam/tagBamMain.cpp | 2 +-
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/src/multiBamCov/multiBamCovMain.cpp b/src/multiBamCov/multiBamCovMain.cpp
index 0491f3ac..55d93cbd 100644
--- a/src/multiBamCov/multiBamCovMain.cpp
+++ b/src/multiBamCov/multiBamCovMain.cpp
@@ -117,9 +117,10 @@ void ShowHelp(void) {
cerr << "\t-bed\t" << "The bed file." << endl << endl;
- cerr << "\t-q [INT]\t" << "Minimum mapping quality allowed. Default is 0." << endl << endl;
+ cerr << "\t-q\t" << "Minimum mapping quality allowed. Default is 0." << endl << endl;
- cerr << "\t-p\t" << "Omly count proper pairs. Default is to count all alignments >= -q" << endl << endl;
+ cerr << "\t-p\t" << "Only count proper pairs. Default is to count all alignments with MAPQ" << endl;
+ cerr << "\t\t" << "greater than the -q argument, regardless of the BAM FLAG field." << endl << endl;
// end the program here
exit(1);
diff --git a/src/tagBam/tagBamMain.cpp b/src/tagBam/tagBamMain.cpp
index 9bd0cebb..d2c1a5b5 100644
--- a/src/tagBam/tagBamMain.cpp
+++ b/src/tagBam/tagBamMain.cpp
@@ -152,7 +152,7 @@ void ShowHelp(void) {
cerr << "Summary: Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files" << endl;
cerr << "\t on the intervals in -i." << endl << endl;
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <BAM> -files FILE1 FILE2 .. FILEn -labels LAB1 LAB2 ,,, LABn" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <BAM> -files FILE1 .. FILEn -labels LAB1 .. LABn" << endl << endl;
cerr << "Options: " << endl;
--
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