From d3587987e517569a4125d765fc9ec84384e2372b Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Thu, 8 May 2014 16:44:52 -0400
Subject: [PATCH] Fixed map and merge help messages.
---
src/mapFile/mapMain.cpp | 4 ++++
src/mergeFile/mergeMain.cpp | 3 +++
src/utils/KeyListOps/KeyListOps.cpp | 3 ---
3 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/src/mapFile/mapMain.cpp b/src/mapFile/mapMain.cpp
index 49d1b270..933fe0c1 100644
--- a/src/mapFile/mapMain.cpp
+++ b/src/mapFile/mapMain.cpp
@@ -48,6 +48,10 @@ void map_help(void) {
cerr << "Options: " << endl;
+ cerr << "\t-c\t" << "Specify columns from the B file to map onto intervals in A." << endl;
+ cerr << "\t\tDefault: 5." << endl;
+ cerr << "\t\tMultiple columns can be specified in a comma-delimited list." << endl << endl;
+
KeyListOpsHelp();
diff --git a/src/mergeFile/mergeMain.cpp b/src/mergeFile/mergeMain.cpp
index cf6804e0..2bee4e32 100644
--- a/src/mergeFile/mergeMain.cpp
+++ b/src/mergeFile/mergeMain.cpp
@@ -66,6 +66,9 @@ void merge_help(void) {
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;
+ cerr << "\t-c\t" << "Specify columns from the input file to operate upon (see -o option, below)." << endl;
+ cerr << "\t\tMultiple columns can be specified in a comma-delimited list." << endl << endl;
+
KeyListOpsHelp();
cerr << "Notes: " << endl;
cerr << "\t(1) All output, regardless of input type (e.g., GFF or VCF)" << endl;
diff --git a/src/utils/KeyListOps/KeyListOps.cpp b/src/utils/KeyListOps/KeyListOps.cpp
index 58544ef3..c71e2425 100644
--- a/src/utils/KeyListOps/KeyListOps.cpp
+++ b/src/utils/KeyListOps/KeyListOps.cpp
@@ -376,9 +376,6 @@ const QuickString & KeyListOps::getOpVals(RecordKeyList &hits)
}
void KeyListOpsHelp() {
- cerr << "\t-c\t" << "Specify columns from the B file to map onto intervals in A." << endl;
- cerr << "\t\tDefault: 5." << endl;
- cerr << "\t\tMultiple columns can be specified in a comma-delimited list." << endl << endl;
cerr << "\t-o\t" << "Specify the operation that should be applied to -c." << endl;
cerr << "\t\tValid operations:" << endl;
--
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