From da54ba34a3da91d74973d2119f143967a144672d Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 14 Jun 2011 09:53:21 -0400
Subject: [PATCH] mergeBed now _always_ reports in BED format (i.e., zero-based
starts), regardless of input type.
---
src/mergeBed/mergeBed.cpp | 6 ++++--
src/mergeBed/mergeMain.cpp | 13 +++++++++----
src/utils/bedFile/bedFile.h | 3 +--
3 files changed, 14 insertions(+), 8 deletions(-)
diff --git a/src/mergeBed/mergeBed.cpp b/src/mergeBed/mergeBed.cpp
index 934a1bca..393eefea 100644
--- a/src/mergeBed/mergeBed.cpp
+++ b/src/mergeBed/mergeBed.cpp
@@ -168,7 +168,8 @@ BedMerge::~BedMerge(void) {
void BedMerge::Report(string chrom, int start, int end,
const vector<string> &names, const vector<string> &scores, int mergeCount)
{
- if (_bed->isZeroBased == false) {start++;}
+ // ARQ: removed to force all output to be zero-based, BED format, reagrdless of input type
+ //if (_bed->isZeroBased == false) {start++;}
printf("%s\t%d\t%d", chrom.c_str(), start, end);
// just the merged intervals
@@ -205,7 +206,8 @@ void BedMerge::ReportStranded(string chrom, int start, int end,
const vector<string> &names, const vector<string> &scores,
int mergeCount, string strand)
{
- if (_bed->isZeroBased == false) {start++;}
+ // ARQ: removed to force all output to be zero-based, BED format, reagrdless of input type
+ //if (_bed->isZeroBased == false) {start++;}
printf("%s\t%d\t%d", chrom.c_str(), start, end);
// just the merged intervals
diff --git a/src/mergeBed/mergeMain.cpp b/src/mergeBed/mergeMain.cpp
index fc435843..03ee9355 100644
--- a/src/mergeBed/mergeMain.cpp
+++ b/src/mergeBed/mergeMain.cpp
@@ -145,12 +145,17 @@ void ShowHelp(void) {
cerr << "\t-nms\t" << "Report the names of the merged features separated by semicolons." << endl << endl;
- cerr << "\t-scores [STRING]\t" << "Report the scores of the merged features. Specify one of " << endl;
+ cerr << "\t-scores\t" << "Report the scores of the merged features. Specify one of " << endl;
cerr << "\t\tthe following options for reporting scores:" << endl;
- cerr << "\t\t\t sum, min, max," << endl;
- cerr << "\t\t\t mean, median, mode, antimode," << endl;
- cerr << "\t\t\t collapse (i.e., print a semicolon-separated list)," << endl << endl;
+ cerr << "\t\t sum, min, max," << endl;
+ cerr << "\t\t mean, median, mode, antimode," << endl;
+ cerr << "\t\t collapse (i.e., print a semicolon-separated list)," << endl;
+ cerr << "\t\t- (INTEGER)" << endl << 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;
+
// end the program here
exit(1);
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index 491d7bca..8d80113f 100644
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -697,7 +697,6 @@ private:
if (numFields == this->bedType) {
if (this->bedType >= 8 && _isGff) {
bed.chrom = lineVector[0];
- // substract 1 to force the start to be BED-style
bed.start = atoi(lineVector[3].c_str());
bed.end = atoi(lineVector[4].c_str());
bed.name = lineVector[2];
@@ -714,7 +713,7 @@ private:
bed.end++;
bed.zeroLength = true;
}
- // GFF uses 1-based starts
+ // GFF uses 1-based starts, covert to zero-based
bed.start--;
}
else {
--
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