From 560ed7f07d12e80510e80146690583cb99c4b95f Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 26 Apr 2010 12:43:54 -0400
Subject: [PATCH] Updated usage statement for pairToBed.
---
src/pairToBed/pairToBedMain.cpp | 20 +++++++++++++-------
1 file changed, 13 insertions(+), 7 deletions(-)
diff --git a/src/pairToBed/pairToBedMain.cpp b/src/pairToBed/pairToBedMain.cpp
index 487ac10d..b263c36a 100755
--- a/src/pairToBed/pairToBedMain.cpp
+++ b/src/pairToBed/pairToBedMain.cpp
@@ -136,6 +136,11 @@ int main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****ERROR: Cannot enforce strandedness with selected searchtype" << endl << "*****" << endl;
showHelp = true;
}
+
+ if (useEditDistance && (inputIsBam == false || outputIsBam == true)) {
+ cerr << endl << "*****" << endl << "*****ERROR: -ed must be used with -bedpe and -abam." << endl << "*****" << endl;
+ showHelp = true;
+ }
if (!showHelp) {
@@ -163,16 +168,17 @@ void ShowHelp(void) {
cerr << "Options: " << endl;
- cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
-
+ cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl;
+ cerr << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl;
+
cerr << "\t-bedpe\t" << "When using BAM input (-abam), write output as BEDPE. The default" << endl;
cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
- cerr << "\t-ed\t" << "Use BAM total edit distance (NM tag) for BEDPE score." << endl;
- cerr << "\t\t- Default for BEDPE is to use the minimum of" << endl;
- cerr << "\t\t of the two mapping qualities for the pair." << endl;
- cerr << "\t\t- When -ed is used the total edit distance" << endl;
- cerr << "\t\t from the two mates is reported as the score." << endl << endl;
+ cerr << "\t-ed\t" << "Use BAM total edit distance (NM tag) for BEDPE score." << endl;
+ cerr << "\t\t- Default for BEDPE is to use the minimum of" << endl;
+ cerr << "\t\t of the two mapping qualities for the pair." << endl;
+ cerr << "\t\t- When -ed is used the total edit distance" << endl;
+ cerr << "\t\t from the two mates is reported as the score." << endl << endl;
cerr << "\t-f\t" << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
cerr << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
--
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