From 054fc8576a192086d718f81c929c587f02fe8dc2 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Thu, 3 Nov 2011 15:50:00 -0400
Subject: [PATCH] Updated banner and help for multiIntersectBed.
---
src/multiIntersectBed/multiIntersectBed.cpp | 14 +-
.../multiIntersectBedMain.cpp | 134 +++++++++---------
2 files changed, 74 insertions(+), 74 deletions(-)
diff --git a/src/multiIntersectBed/multiIntersectBed.cpp b/src/multiIntersectBed/multiIntersectBed.cpp
index a0738f61..e4eb5e10 100644
--- a/src/multiIntersectBed/multiIntersectBed.cpp
+++ b/src/multiIntersectBed/multiIntersectBed.cpp
@@ -123,14 +123,12 @@ void MultiIntersectBed::UpdateInformation(const IntervalItem &item) {
case START:
current_depth[item.source_index] = 1;
current_non_zero_inputs++;
- files_with_coverage[item.source_index] = true;
break;
case END:
//Read the next interval from this file
AddInterval(item.source_index);
current_depth[item.source_index] = 0;
current_non_zero_inputs--;
- files_with_coverage.erase(item.source_index);
break;
default:
assert(0);
@@ -162,9 +160,15 @@ void MultiIntersectBed::AddInterval(int index) {
void MultiIntersectBed::PrintHeader() {
- output << "chrom\tstart\tend\tnum\tlist" ;
- for (size_t i=0;i<titles.size();++i)
- output << "\t" <<titles[i];
+ output << "chrom\tstart\tend\tnum\tlist";
+ if (titles.size() > 0) {
+ for (size_t i = 0; i < titles.size(); ++i)
+ output << "\t" << titles[i];
+ }
+ else {
+ for (size_t i = 0;i < filenames.size(); ++i)
+ output << "\t" << filenames[i];
+ }
output << endl;
}
diff --git a/src/multiIntersectBed/multiIntersectBedMain.cpp b/src/multiIntersectBed/multiIntersectBedMain.cpp
index 884af23c..5248315e 100644
--- a/src/multiIntersectBed/multiIntersectBedMain.cpp
+++ b/src/multiIntersectBed/multiIntersectBedMain.cpp
@@ -136,11 +136,11 @@ int main(int argc, char* argv[])
//Sanity checks
if (inputFiles.empty() == true) {
- cerr << "Error: missing BedGraph file names (-i) to combine." << endl;
+ cerr << "Error: missing file names (-i) to combine." << endl;
exit(1);
}
if (inputFiles.size() == 1) {
- cerr << "Error: Only a single BedGraph file was specified. Nothing to combine, exiting." << endl;
+ cerr << "Error: Only a single file was specified. Nothing to combine, exiting." << endl;
exit(1);
}
if (printEmptyRegions && (genomeFile.empty() == true)) {
@@ -162,15 +162,14 @@ void ShowHelp(void) {
cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "Authors: Assaf Gordon, CSHL" << endl;
- cerr << " Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl;
+ cerr << "Authors: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
+ cerr << " Assaf Gordon" << endl << endl;
- cerr << "Summary: Combines multiple BedGraph files into a single file," << endl;
- cerr << "\t allowing coverage comparisons between them." << endl << endl;
+ cerr << "Summary: Identifies common intervals among multiple" << endl;
+ cerr << "\t BED/GFF/VCF files." << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i FILE1 FILE2 .. FILEn" << endl;
- cerr << "\t Assumes that each BedGraph file is sorted by chrom/start " << endl;
- cerr << "\t and that the intervals in each are non-overlapping." << endl << endl;
+ cerr << "\t Requires that each interval file is sorted by chrom/start. " << endl << endl;
cerr << "Options: " << endl;
@@ -200,79 +199,77 @@ void ShowExamples()
cerr << "Example usage:\n\n" \
"== Input files: ==\n" \
"\n" \
-" $ cat 1.bg\n" \
-" chr1 1000 1500 10\n" \
-" chr1 2000 2100 20\n" \
+" $ cat a.bed\n" \
+" chr1 6 12\n" \
+" chr1 10 20\n" \
+" chr1 22 27\n" \
+" chr1 24 30\n" \
"\n" \
-" $ cat 2.bg\n" \
-" chr1 900 1600 60\n" \
-" chr1 1700 2050 50\n" \
+" $ cat b.bed\n" \
+" chr1 12 32\n" \
+" chr1 14 30\n" \
"\n" \
-" $ cat 3.bg\n" \
-" chr1 1980 2070 80\n" \
-" chr1 2090 2100 20\n" \
+" $ cat c.bed\n" \
+" chr1 8 15\n" \
+" chr1 10 14\n" \
+" chr1 32 34\n" \
"\n" \
" $ cat sizes.txt\n" \
" chr1 5000\n" \
"\n" \
-"== Union/combine the files: ==\n" \
+"== Multi-intersect the files: ==\n" \
"\n" \
-" $ unionBedGraphs -i 1.bg 2.bg 3.bg\n" \
-" chr1 900 1000 0 60 0\n" \
-" chr1 1000 1500 10 60 0\n" \
-" chr1 1500 1600 0 60 0\n" \
-" chr1 1700 1980 0 50 0\n" \
-" chr1 1980 2000 0 50 80\n" \
-" chr1 2000 2050 20 50 80\n" \
-" chr1 2050 2070 20 0 80\n" \
-" chr1 2070 2090 20 0 0\n" \
-" chr1 2090 2100 20 0 20\n" \
+" $ multiIntersectBed -i a.bed b.bed c.bed\n" \
+"chr1 6 8 1 1 1 0 0\n" \
+"chr1 8 12 2 1,3 1 0 1\n" \
+"chr1 12 15 3 1,2,3 1 1 1\n" \
+"chr1 15 20 2 1,2 1 1 0\n" \
+"chr1 20 22 1 2 0 1 0\n" \
+"chr1 22 30 2 1,2 1 1 0\n" \
+"chr1 30 32 1 2 0 1 0\n" \
+"chr1 32 34 1 3 0 0 1\n" \
"\n" \
-"== Union/combine the files, with a header line (titles are the file names): ==\n" \
+"== Multi-intersect the files, with a header line (titles are the file names): ==\n" \
"\n" \
-" $ unionBedGraphs -header -i 1.bg 2.bg 3.bg\n" \
-" chrom start end 1 2 3\n" \
-" chr1 900 1000 0 60 0\n" \
-" chr1 1000 1500 10 60 0\n" \
-" chr1 1500 1600 0 60 0\n" \
-" chr1 1700 1980 0 50 0\n" \
-" chr1 1980 2000 0 50 80\n" \
-" chr1 2000 2050 20 50 80\n" \
-" chr1 2050 2070 20 0 80\n" \
-" chr1 2070 2090 20 0 0\n" \
-" chr1 2090 2100 20 0 20\n" \
+" $ multiIntersectBed -header -i a.bed b.bed c.bed\n" \
+" chrom start end num list a.bed b.bed c.bed\n" \
+" chr1 6 8 1 1 1 0 0\n" \
+" chr1 8 12 2 1,3 1 0 1\n" \
+" chr1 12 15 3 1,2,3 1 1 1\n" \
+" chr1 15 20 2 1,2 1 1 0\n" \
+" chr1 20 22 1 2 0 1 0\n" \
+" chr1 22 30 2 1,2 1 1 0\n" \
+" chr1 30 32 1 2 0 1 0\n" \
+" chr1 32 34 1 3 0 0 1\n" \
"\n" \
-"== Union/combine the files, with a header line and custom names: ==\n" \
+"== Multi-intersect the files, with a header line and custom names: ==\n" \
"\n" \
-" $ unionBedGraphs -header -i 1.bg 2.bg 3.bg -names WT-1 WT-2 KO-1\n" \
-" chrom start end WT-1 WT-2 KO-1\n" \
-" chr1 900 1000 0 60 0\n" \
-" chr1 1000 1500 10 60 0\n" \
-" chr1 1500 1600 0 60 0\n" \
-" chr1 1700 1980 0 50 0\n" \
-" chr1 1980 2000 0 50 80\n" \
-" chr1 2000 2050 20 50 80\n" \
-" chr1 2050 2070 20 0 80\n" \
-" chr1 2070 2090 20 0 0\n" \
-" chr1 2090 2100 20 0 20\n" \
+" $ multiIntersectBed -header -i a.bed b.bed c.bed -names A B C\n" \
+" chrom start end num list A B C\n" \
+" chr1 6 8 1 A 1 0 0\n" \
+" chr1 8 12 2 A,C 1 0 1\n" \
+" chr1 12 15 3 A,B,C 1 1 1\n" \
+" chr1 15 20 2 A,B 1 1 0\n" \
+" chr1 20 22 1 B 0 1 0\n" \
+" chr1 22 30 2 A,B 1 1 0\n" \
+" chr1 30 32 1 B 0 1 0\n" \
+" chr1 32 34 1 C 0 0 1\n" \
"\n" \
-"== Union/combine, showing empty regions (note, requires -g): ==\n" \
-"\n" \
-" $ unionBedGraphs -header -empty -g sizes.TXT -i 1.bg 2.bg 3.bg\n" \
-" chrom start end 1 2 3\n" \
-" chr1 0 900 0 0 0\n" \
-" chr1 900 1000 0 60 0\n" \
-" chr1 1000 1500 10 60 0\n" \
-" chr1 1500 1600 0 60 0\n" \
-" chr1 1600 1700 0 0 0\n" \
-" chr1 1700 1980 0 50 0\n" \
-" chr1 1980 2000 0 50 80\n" \
-" chr1 2000 2050 20 50 80\n" \
-" chr1 2050 2070 20 0 80\n" \
-" chr1 2070 2090 20 0 0\n" \
-" chr1 2090 2100 20 0 20\n" \
-" chr1 2100 5000 0 0 0\n" \
+"== Multi-intersect the files, showing empty regions (note, requires -g): ==\n" \
"\n" \
+" $ multiIntersectBed -header -i a.bed b.bed c.bed -names A B C -empty -g sizes.txt\n" \
+" chrom start end num list A B C\n" \
+" chr1 0 6 0 none 0 0 0\n" \
+" chr1 6 8 1 A 1 0 0\n" \
+" chr1 8 12 2 A,C 1 0 1\n" \
+" chr1 12 15 3 A,B,C 1 1 1\n" \
+" chr1 15 20 2 A,B 1 1 0\n" \
+" chr1 20 22 1 B 0 1 0\n" \
+" chr1 22 30 2 A,B 1 1 0\n" \
+" chr1 30 32 1 B 0 1 0\n" \
+" chr1 32 34 1 C 0 0 1\n" \
+" chr1 34 5000 0 none 0 0 0\n" \
+"\n"
;
}
@@ -291,4 +288,3 @@ std::string stl_basename(const std::string& path)
return result;
}
-
--
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