From 9fc914ad4f637d1a4368a7f0fd7c591cc2843869 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Fri, 24 Jun 2011 11:57:11 -0400
Subject: [PATCH] User can define their own tag type for tagBam.
---
src/tagBam/tagBam.cpp | 6 ++++--
src/tagBam/tagBam.h | 4 +++-
src/tagBam/tagBamMain.cpp | 24 ++++++++++++++++++++----
3 files changed, 27 insertions(+), 7 deletions(-)
diff --git a/src/tagBam/tagBam.cpp b/src/tagBam/tagBam.cpp
index 8ad1ded4..56174357 100644
--- a/src/tagBam/tagBam.cpp
+++ b/src/tagBam/tagBam.cpp
@@ -14,11 +14,13 @@
// build
TagBam::TagBam(const string &bamFile, const vector<string> &annoFileNames,
- const vector<string> &annoLables, bool forceStrand, float overlapFraction) :
+ const vector<string> &annoLables, const string &tag,
+ bool forceStrand, float overlapFraction) :
_bamFile(bamFile),
_annoFileNames(annoFileNames),
_annoLabels(annoLables),
+ _tag(tag),
_forceStrand(forceStrand),
_overlapFraction(overlapFraction)
{}
@@ -97,7 +99,7 @@ void TagBam::Tag() {
}
// were there any overlaps with which to make a tag?
if (annotations.str().size() > 0) {
- al.AddTag("YB", "Z", annotations.str().substr(0, annotations.str().size() - 1)); // get rid of the last ";"
+ al.AddTag(_tag, "Z", annotations.str().substr(0, annotations.str().size() - 1)); // get rid of the last ";"
}
writer.SaveAlignment(al);
}
diff --git a/src/tagBam/tagBam.h b/src/tagBam/tagBam.h
index 10295ea0..821d0044 100644
--- a/src/tagBam/tagBam.h
+++ b/src/tagBam/tagBam.h
@@ -40,7 +40,8 @@ public:
// constructor
TagBam(const string &bamFile, const vector<string> &annoFileNames,
- const vector<string> &annoLabels, bool forceStrand, float overlapFraction);
+ const vector<string> &annoLabels, const string &tag,
+ bool forceStrand, float overlapFraction);
// destructor
~TagBam(void);
@@ -54,6 +55,7 @@ private:
string _bamFile;
vector<string> _annoFileNames;
vector<string> _annoLabels;
+ string _tag;
// instance of a bed file class.
BedFile *_bed;
diff --git a/src/tagBam/tagBamMain.cpp b/src/tagBam/tagBamMain.cpp
index 5eaddfea..9bd0cebb 100644
--- a/src/tagBam/tagBamMain.cpp
+++ b/src/tagBam/tagBamMain.cpp
@@ -31,9 +31,11 @@ int main(int argc, char* argv[]) {
// input file
string bamFile;
float overlapFraction = 1E-9;
+ string tag = "YB";
// parm flags
- bool haveFraction = false;
+ bool haveTag = false;
+ bool haveFraction = false;
bool forceStrand = false;
bool haveBam = false;
bool haveFiles = false;
@@ -83,7 +85,7 @@ int main(int argc, char* argv[]) {
i--;
}
}
- else if(PARAMETER_CHECK("-tags", 5, parameterLength)) {
+ else if(PARAMETER_CHECK("-labels", 7, parameterLength)) {
if ((i+1) < argc) {
haveLabels = true;
i = i+1;
@@ -107,6 +109,13 @@ int main(int argc, char* argv[]) {
i++;
}
}
+ else if(PARAMETER_CHECK("-tag", 4, parameterLength)) {
+ if ((i+1) < argc) {
+ haveTag = true;
+ tag = argv[i + 1];
+ i++;
+ }
+ }
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
@@ -118,9 +127,13 @@ int main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****ERROR: Need -i, -files, and -labels. " << endl << "*****" << endl;
showHelp = true;
}
+ if (haveTag && tag.size() > 2) {
+ cerr << endl << "*****" << endl << "*****ERROR: Custom tags should be at most two characters per the SAM specification. " << endl << "*****" << endl;
+ showHelp = true;
+ }
if (!showHelp) {
- TagBam *ba = new TagBam(bamFile, inputFiles, inputLabels, forceStrand, overlapFraction);
+ TagBam *ba = new TagBam(bamFile, inputFiles, inputLabels, tag, forceStrand, overlapFraction);
ba->Tag();
delete ba;
return 0;
@@ -139,7 +152,7 @@ void ShowHelp(void) {
cerr << "Summary: Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files" << endl;
cerr << "\t on the intervals in -i." << endl << endl;
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <BAM> -files FILE1 FILE2 .. FILEn -tags LAB1 LAB2 ,,, LABn" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <BAM> -files FILE1 FILE2 .. FILEn -labels LAB1 LAB2 ,,, LABn" << endl << endl;
cerr << "Options: " << endl;
@@ -149,6 +162,9 @@ void ShowHelp(void) {
cerr << "\t-f\t" << "Minimum overlap required as a fraction of the alignment." << endl;
cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
+
+ cerr << "\t-tag\t" << "Dictate what the tag should be. Default is YB." << endl;
+ cerr << "\t\t- STRING (two characters, e.g., YK)" << endl << endl;
exit(1);
}
--
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