From 4fd41ae5e003307b46aa50ab58bc07af3a6287f4 Mon Sep 17 00:00:00 2001
From: arq5x <arq5x@virginia.edu>
Date: Thu, 17 Apr 2014 13:07:55 -0400
Subject: [PATCH] add missing help menu items (-S -header) to merge
---
src/mergeFile/mergeMain.cpp | 21 ++++++++++++---------
1 file changed, 12 insertions(+), 9 deletions(-)
diff --git a/src/mergeFile/mergeMain.cpp b/src/mergeFile/mergeMain.cpp
index 0318725a..2e74b894 100644
--- a/src/mergeFile/mergeMain.cpp
+++ b/src/mergeFile/mergeMain.cpp
@@ -52,19 +52,22 @@ void merge_help(void) {
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl;
cerr << "Options: " << endl;
- cerr << "\t-s\t" << "Force strandedness. That is, only merge features" << endl;
- cerr << "\t\tthat are the same strand." << endl;
- cerr << "\t\t- By default, merging is done without respect to strand." << endl << endl;
+ cerr << "\t-s\t" << "Force strandedness. That is, only merge features" << endl;
+ cerr << "\t\tthat are the same strand." << endl;
+ cerr << "\t\t- By default, merging is done without respect to strand." << endl << endl;
+ cerr << "\t-S\t" << "Force mergeing for a _specific_ strand. That is, only merge features" << endl;
+ cerr << "\t\tthat from a specific strabd." << endl;
+ cerr << "\t\t- For example, -S + will or -S -" << endl;
+ cerr << "\t\t- By default, merging is done without respect to strand." << endl << endl;
- cerr << "\t-d\t" << "Maximum distance between features allowed for features" << endl;
- cerr << "\t\tto be merged." << endl;
- cerr << "\t\t- Def. 0. That is, overlapping & book-ended features are merged." << endl;
- cerr << "\t\t- (INTEGER)" << endl << endl;
+ cerr << "\t-d\t" << "Maximum distance between features allowed for features" << endl; cerr << "\t\tto be merged." << endl; cerr << "\t\t- Def. 0. That is, overlapping & book-ended features are merged." << endl;
+ cerr << "\t\t- (INTEGER)" << endl;
+ cerr << "\t\t- Note: negative values enforce the number of b.p. required for overlap." << endl << endl;
+ cerr << "\t-header\t" << "Print the header from the A file prior to results." << endl << endl;
KeyListOpsHelp();
-
- cerr << "Notes: " << endl;
+ cerr << "Notes: " << endl;
cerr << "\t(1) All output, regardless of input type (e.g., GFF or VCF)" << endl;
cerr << "\t will in BED format with zero-based starts" << endl << endl;
--
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