From f2433c5c78ac5eab63a871635de38cf69a582f5a Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 5 Sep 2011 11:02:49 -0400
Subject: [PATCH] Added -s, -S, and -names to tagBam.
---
src/tagBam/tagBam.cpp | 33 +++++++++++++++++++++++----------
src/tagBam/tagBam.h | 11 +++++++----
src/tagBam/tagBamMain.cpp | 39 +++++++++++++++++++++++++++++++++------
3 files changed, 63 insertions(+), 20 deletions(-)
diff --git a/src/tagBam/tagBam.cpp b/src/tagBam/tagBam.cpp
index 56174357..d06cf9ed 100644
--- a/src/tagBam/tagBam.cpp
+++ b/src/tagBam/tagBam.cpp
@@ -15,13 +15,15 @@
// build
TagBam::TagBam(const string &bamFile, const vector<string> &annoFileNames,
const vector<string> &annoLables, const string &tag,
- bool forceStrand, float overlapFraction) :
+ bool useNames, bool sameStrand, bool diffStrand, float overlapFraction):
_bamFile(bamFile),
_annoFileNames(annoFileNames),
_annoLabels(annoLables),
_tag(tag),
- _forceStrand(forceStrand),
+ _useNames(useNames),
+ _sameStrand(sameStrand),
+ _diffStrand(diffStrand),
_overlapFraction(overlapFraction)
{}
@@ -50,10 +52,6 @@ void TagBam::CloseAnnoFiles() {
}
}
-bool TagBam::FindOneOrMoreOverlap(const BED &a, BedFile *bedFile) {
- return bedFile->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand,
- _forceStrand, _overlapFraction);
-}
void TagBam::Tag() {
@@ -77,14 +75,15 @@ void TagBam::Tag() {
// rip through the BAM file and test for overlaps with each annotation file.
BamAlignment al;
+ vector<BED> hits;
while (reader.GetNextAlignment(al)) {
if (al.IsMapped() == true) {
BED a;
a.chrom = refs.at(al.RefID).RefName;
a.start = al.Position;
a.end = al.GetEndPosition(false, false);
- if (al.IsReverseStrand()) a.strand = "-";
a.strand = "+";
+ if (al.IsReverseStrand()) a.strand = "-";
ostringstream annotations;
// annotate the BAM file based on overlaps with the annotation files.
@@ -92,9 +91,23 @@ void TagBam::Tag() {
{
// grab the current annotation file.
BedFile *anno = _annoFiles[i];
- // add the label for this annotation file to tag if there is overlap
- if (FindOneOrMoreOverlap(a, anno)) {
- annotations << _annoLabels[i] << ";";
+
+ if (!_useNames) {
+ // add the label for this annotation file to tag if there is overlap
+ if (anno->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand, _sameStrand, _diffStrand, _overlapFraction))
+ {
+ annotations << _annoLabels[i] << ";";
+ }
+ }
+ // use the name field from the annotation files to populate tag
+ else {
+ anno->FindOverlapsPerBin(a.chrom, a.start, a.end, a.strand, hits, _sameStrand, _diffStrand);
+ for (size_t i = 0; i < hits.size(); ++i) {
+ annotations << hits[i].name;
+ if (i < hits.size() - 1) annotations << ",";
+ }
+ if (hits.size() > 0) annotations << ";";
+ hits.clear();
}
}
// were there any overlaps with which to make a tag?
diff --git a/src/tagBam/tagBam.h b/src/tagBam/tagBam.h
index 821d0044..10ade9ad 100644
--- a/src/tagBam/tagBam.h
+++ b/src/tagBam/tagBam.h
@@ -41,7 +41,7 @@ public:
// constructor
TagBam(const string &bamFile, const vector<string> &annoFileNames,
const vector<string> &annoLabels, const string &tag,
- bool forceStrand, float overlapFraction);
+ bool useNames, bool sameStrand, bool diffStrand, float overlapFraction);
// destructor
~TagBam(void);
@@ -61,8 +61,12 @@ private:
BedFile *_bed;
vector<BedFile*> _annoFiles;
+ // should we use the name field from the annotation files?
+ bool _useNames;
+
// do we care about strandedness when tagging?
- bool _forceStrand;
+ bool _sameStrand;
+ bool _diffStrand;
float _overlapFraction;
// private function for reporting coverage information
@@ -71,7 +75,6 @@ private:
void OpenAnnoFiles();
void CloseAnnoFiles();
-
- bool FindOneOrMoreOverlap(const BED &a, BedFile *bedFile);
+
};
#endif /* TAGBAM_H */
diff --git a/src/tagBam/tagBamMain.cpp b/src/tagBam/tagBamMain.cpp
index d2c1a5b5..acd9c70e 100644
--- a/src/tagBam/tagBamMain.cpp
+++ b/src/tagBam/tagBamMain.cpp
@@ -36,7 +36,9 @@ int main(int argc, char* argv[]) {
// parm flags
bool haveTag = false;
bool haveFraction = false;
- bool forceStrand = false;
+ bool useNames = false;
+ bool sameStrand = false;
+ bool diffStrand = false;
bool haveBam = false;
bool haveFiles = false;
bool haveLabels = false;
@@ -99,8 +101,14 @@ int main(int argc, char* argv[]) {
i--;
}
}
+ else if (PARAMETER_CHECK("-names", 6, parameterLength)) {
+ useNames = true;
+ }
else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
- forceStrand = true;
+ sameStrand = true;
+ }
+ else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
+ diffStrand = true;
}
else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
if ((i+1) < argc) {
@@ -123,8 +131,20 @@ int main(int argc, char* argv[]) {
}
// make sure we have both input files
- if (!haveBam || !haveFiles || !haveLabels) {
- cerr << endl << "*****" << endl << "*****ERROR: Need -i, -files, and -labels. " << endl << "*****" << endl;
+ if (!haveBam || !haveFiles) {
+ cerr << endl << "*****" << endl << "*****ERROR: Need -i, -files" << endl << "*****" << endl;
+ showHelp = true;
+ }
+ if (!useNames && !haveLabels) {
+ cerr << endl << "*****" << endl << "*****ERROR: Need -labels or -names" << endl << "*****" << endl;
+ showHelp = true;
+ }
+ if (sameStrand && diffStrand) {
+ cerr << endl << "*****" << endl << "*****ERROR: Use -s or -S, not both. " << endl << "*****" << endl;
+ showHelp = true;
+ }
+ if (haveLabels && useNames) {
+ cerr << endl << "*****" << endl << "*****ERROR: Use -labels or -names, not both. " << endl << "*****" << endl;
showHelp = true;
}
if (haveTag && tag.size() > 2) {
@@ -133,7 +153,7 @@ int main(int argc, char* argv[]) {
}
if (!showHelp) {
- TagBam *ba = new TagBam(bamFile, inputFiles, inputLabels, tag, forceStrand, overlapFraction);
+ TagBam *ba = new TagBam(bamFile, inputFiles, inputLabels, tag, useNames, sameStrand, diffStrand, overlapFraction);
ba->Tag();
delete ba;
return 0;
@@ -156,7 +176,10 @@ void ShowHelp(void) {
cerr << "Options: " << endl;
- cerr << "\t-s\t" << "Force strandedness. That is, only tag alignments that have the same" << endl;
+ cerr << "\t-s\t" << "Require overlaps on the same strand. That is, only tag alignments that have the same" << endl;
+ cerr << "\t\tstrand as a feature in the annotation file(s)." << endl << endl;
+
+ cerr << "\t-S\t" << "Require overlaps on the opposite strand. That is, only tag alignments that have the opposite" << endl;
cerr << "\t\tstrand as a feature in the annotation file(s)." << endl << endl;
cerr << "\t-f\t" << "Minimum overlap required as a fraction of the alignment." << endl;
@@ -166,5 +189,9 @@ void ShowHelp(void) {
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;
+ cerr << "\t-names\t" << "Use the name field from the annotation files to populate tags." << endl;
+ cerr << "\t\tBy default, the -labels values are used." << endl << endl;
+
+
exit(1);
}
--
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