From 8c37692fc04fd77d958fcfa2954ae48b47cc66f2 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 21 Sep 2010 10:26:42 -0400
Subject: [PATCH] annotateBed can report counts and pct coverage for each
annotation file.
---
src/annotateBed/annotateBed.cpp | 15 +++++++++++----
src/annotateBed/annotateMain.cpp | 2 +-
2 files changed, 12 insertions(+), 5 deletions(-)
diff --git a/src/annotateBed/annotateBed.cpp b/src/annotateBed/annotateBed.cpp
index ad46f3c7..269dcd9b 100644
--- a/src/annotateBed/annotateBed.cpp
+++ b/src/annotateBed/annotateBed.cpp
@@ -60,9 +60,16 @@ void BedAnnotate::PrintHeader() {
printf("\t");
// now print the label for each file.
- for (size_t i = 0; i < _annoTitles.size(); ++i)
- printf("%s\t", _annoTitles[i].c_str());
- printf("\n");
+ if (_reportBoth == false) {
+ for (size_t i = 0; i < _annoTitles.size(); ++i)
+ printf("%s\t", _annoTitles[i].c_str());
+ printf("\n");
+ }
+ else {
+ for (size_t i = 0; i < _annoTitles.size(); ++i)
+ printf("%s_cnt\t%s_pct", _annoTitles[i].c_str(), _annoTitles[i].c_str());
+ printf("\n");
+ }
}
@@ -189,7 +196,7 @@ void BedAnnotate::ReportAnnotations() {
else if (_reportCounts == true && _reportBoth == false)
printf("%d\t", bedItr->counts[i]);
else if (_reportCounts == false && _reportBoth == true)
- printf("%d,%f\t", bedItr->counts[i], fractCovered);
+ printf("%d\t%f\t", bedItr->counts[i], fractCovered);
}
// print newline for next feature.
printf("\n");
diff --git a/src/annotateBed/annotateMain.cpp b/src/annotateBed/annotateMain.cpp
index 3bdd1e4e..439c84dc 100644
--- a/src/annotateBed/annotateMain.cpp
+++ b/src/annotateBed/annotateMain.cpp
@@ -148,7 +148,7 @@ void ShowHelp(void) {
cerr << "\t-counts\t" << "Report the count of features in each file that overlap -i." << endl;
cerr << "\t\t- Default is to report the fraction of -i covered by each file." << endl << endl;
- cerr << "\t-both\t" << "Report the counts and % coverage." << endl;
+ cerr << "\t-both\t" << "Report the counts followed by the % coverage." << endl;
cerr << "\t\t- Default is to report the fraction of -i covered by each file." << endl << endl;
cerr << "\t-s\t" << "Force strandedness. That is, only include hits in A that" << endl;
--
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