diff --git a/src/tagBam/tagBam.cpp b/src/tagBam/tagBam.cpp
index d06cf9ede54d65c92918a9f9d1f9e0a9eb5389a9..36a2c4d11e582efff9fa067d8aaae872fbd2503d 100644
--- a/src/tagBam/tagBam.cpp
+++ b/src/tagBam/tagBam.cpp
@@ -15,13 +15,14 @@
// build
TagBam::TagBam(const string &bamFile, const vector<string> &annoFileNames,
const vector<string> &annoLables, const string &tag,
- bool useNames, bool sameStrand, bool diffStrand, float overlapFraction):
+ bool useNames, bool useScores, bool sameStrand, bool diffStrand, float overlapFraction):
_bamFile(bamFile),
_annoFileNames(annoFileNames),
_annoLabels(annoLables),
_tag(tag),
_useNames(useNames),
+ _useScores(useScores),
_sameStrand(sameStrand),
_diffStrand(diffStrand),
_overlapFraction(overlapFraction)
@@ -92,15 +93,25 @@ void TagBam::Tag() {
// grab the current annotation file.
BedFile *anno = _annoFiles[i];
- if (!_useNames) {
+ if (!_useNames && !_useScores) {
// 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 score field
+ else if (!_useNames && _useScores) {
+ 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].score;
+ if (i < hits.size() - 1) annotations << ",";
+ }
+ if (hits.size() > 0) annotations << ";";
+ hits.clear();
+ }
// use the name field from the annotation files to populate tag
- else {
+ else if (_useNames && !_useScores) {
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;
diff --git a/src/tagBam/tagBam.h b/src/tagBam/tagBam.h
index 10ade9ad574d03f0f2ac2d9d239766897226af29..689dd0ac31a5acd44fff8e206f78e13bdeabff19 100644
--- a/src/tagBam/tagBam.h
+++ b/src/tagBam/tagBam.h
@@ -40,8 +40,9 @@ public:
// constructor
TagBam(const string &bamFile, const vector<string> &annoFileNames,
- const vector<string> &annoLabels, const string &tag,
- bool useNames, bool sameStrand, bool diffStrand, float overlapFraction);
+ const vector<string> &annoLabels, const string &tag,
+ bool useNames, bool useScores, bool sameStrand,
+ bool diffStrand, float overlapFraction);
// destructor
~TagBam(void);
@@ -55,6 +56,7 @@ private:
string _bamFile;
vector<string> _annoFileNames;
vector<string> _annoLabels;
+
string _tag;
// instance of a bed file class.
@@ -63,6 +65,7 @@ private:
// should we use the name field from the annotation files?
bool _useNames;
+ bool _useScores;
// do we care about strandedness when tagging?
bool _sameStrand;
diff --git a/src/tagBam/tagBamMain.cpp b/src/tagBam/tagBamMain.cpp
index acd9c70ee8e77b76de1e870cc75603c235184b67..6bef5734e67486469b558cd6849e4f2a993be7ec 100644
--- a/src/tagBam/tagBamMain.cpp
+++ b/src/tagBam/tagBamMain.cpp
@@ -34,14 +34,16 @@ int main(int argc, char* argv[]) {
string tag = "YB";
// parm flags
- bool haveTag = false;
- bool haveFraction = false;
- bool useNames = false;
- bool sameStrand = false;
- bool diffStrand = false;
- bool haveBam = false;
- bool haveFiles = false;
- bool haveLabels = false;
+ bool haveTag = false;
+ bool haveFraction = false;
+ bool useNames = false;
+ bool useScores = false;
+ bool sameStrand = false;
+ bool diffStrand = false;
+ bool haveBam = false;
+ bool haveFiles = false;
+ bool haveLabels = false;
+
// list of annotation files / names
vector<string> inputFiles;
@@ -104,6 +106,9 @@ int main(int argc, char* argv[]) {
else if (PARAMETER_CHECK("-names", 6, parameterLength)) {
useNames = true;
}
+ else if (PARAMETER_CHECK("-scores", 7, parameterLength)) {
+ useScores = true;
+ }
else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
sameStrand = true;
}
@@ -135,8 +140,8 @@ int main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****ERROR: Need -i, -files" << endl << "*****" << endl;
showHelp = true;
}
- if (!useNames && !haveLabels) {
- cerr << endl << "*****" << endl << "*****ERROR: Need -labels or -names" << endl << "*****" << endl;
+ if (!useNames && !haveLabels && !useScores) {
+ cerr << endl << "*****" << endl << "*****ERROR: Need -labels or -names or -scores" << endl << "*****" << endl;
showHelp = true;
}
if (sameStrand && diffStrand) {
@@ -147,13 +152,17 @@ int main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****ERROR: Use -labels or -names, not both. " << endl << "*****" << endl;
showHelp = true;
}
+ if (useScores && useNames) {
+ cerr << endl << "*****" << endl << "*****ERROR: Use -scores or -names, not both. " << 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, tag, useNames, sameStrand, diffStrand, overlapFraction);
+ TagBam *ba = new TagBam(bamFile, inputFiles, inputLabels, tag, useNames, useScores, sameStrand, diffStrand, overlapFraction);
ba->Tag();
delete ba;
return 0;
@@ -191,6 +200,9 @@ void ShowHelp(void) {
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;
+
+ cerr << "\t-scores\t" << "A list of 1-based columns for each annotation file" << endl;
+ cerr << "\t\tin which a color can be found." << endl << endl;
exit(1);