Added intervals option to tagBam.

src/tagBam/tagBam.cpp

@@ -15,7 +15,8 @@
 // build
 TagBam::TagBam(const string &bamFile, const vector<string> &annoFileNames,
             const vector<string> &annoLables, const string &tag,
-            bool useNames, bool useScores, bool sameStrand, bool diffStrand, float overlapFraction):
+            bool useNames, bool useScores, bool useIntervals, 
+            bool sameStrand, bool diffStrand, float overlapFraction):
 
     _bamFile(bamFile),
     _annoFileNames(annoFileNames),
@@ -23,6 +24,7 @@ TagBam::TagBam(const string &bamFile, const vector<string> &annoFileNames,
     _tag(tag),
     _useNames(useNames),
     _useScores(useScores),
+    _useIntervals(useIntervals),
     _sameStrand(sameStrand),
     _diffStrand(diffStrand),
     _overlapFraction(overlapFraction)
@@ -94,7 +96,7 @@ void TagBam::Tag() {
                 // grab the current annotation file.
                 BedFile *anno = _annoFiles[i];
                 
-                if (!_useNames && !_useScores) {
+                if (!_useNames && !_useScores && !_useIntervals) {
                     // 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))
                     {
@@ -102,7 +104,7 @@ void TagBam::Tag() {
                     }
                 }
                 // use the score field
-                else if (!_useNames && _useScores) {
+                else if (!_useNames && _useScores && !_useIntervals) {
                     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;
@@ -112,11 +114,27 @@ void TagBam::Tag() {
                     hits.clear();
                 }
                 // use the name field from the annotation files to populate tag
-                else if (_useNames && !_useScores) {
+                else if (_useNames && !_useScores && !_useIntervals) {
                     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 << ",";
+                    for (size_t j = 0; j < hits.size(); ++i) {
+                        annotations << hits[j].name;
+                        if (j < hits.size() - 1) annotations << ",";
+                    }
+                    if (hits.size() > 0) annotations << ";";
+                    hits.clear();
+                }
+                // use the name field from the annotation files to populate tag
+                else if (!_useNames && !_useScores && _useIntervals) {
+                    anno->FindOverlapsPerBin(a.chrom, a.start, a.end, a.strand, hits, _sameStrand, _diffStrand);
+                    for (size_t j = 0; j < hits.size(); ++j) {
+                        annotations << _annoLabels[i]  << ":" << 
+                                        hits[j].chrom  << ":" <<
+                                        hits[j].start  << "-" <<
+                                        hits[j].end    << "," <<
+                                        hits[j].name   << "," <<
+                                        hits[j].score  << "," <<
+                                        hits[j].strand;
+                        if (j < hits.size() - 1) annotations << ",";
                     }
                     if (hits.size() > 0) annotations << ";";
                     hits.clear();
@@ -126,11 +144,11 @@ void TagBam::Tag() {
             if (annotations.str().size() > 0) {
                 al.AddTag(_tag, "Z", annotations.str().substr(0, annotations.str().size() - 1)); // get rid of the last ";"
             }
-            writer.SaveAlignment(al);
         }
+        writer.SaveAlignment(al);
     }
     reader.Close();
-
+    writer.Close();
     // close the annotations files;
     CloseAnnoFiles();
 }

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 useNames, bool useScores, bool sameStrand, 
+                bool useNames, bool useScores, bool useIntervals, bool sameStrand, 
                 bool diffStrand, float overlapFraction);
 
     // destructor
@@ -66,6 +66,7 @@ private:
     // should we use the name field from the annotation files?
     bool _useNames;
     bool _useScores;
+    bool _useIntervals;
     
     // do we care about strandedness when tagging?
     bool _sameStrand;

src/tagBam/tagBamMain.cpp

@@ -38,6 +38,7 @@ int main(int argc, char* argv[]) {
     bool haveFraction     = false;
     bool useNames         = false;
     bool useScores        = false;
+    bool useIntervals     = false;
     bool sameStrand       = false;
     bool diffStrand       = false;
     bool haveBam          = false;
@@ -109,6 +110,9 @@ int main(int argc, char* argv[]) {
         else if (PARAMETER_CHECK("-scores", 7, parameterLength)) {
             useScores = true;
         }
+        else if (PARAMETER_CHECK("-intervals", 10, parameterLength)) {
+            useIntervals = true;
+        }
         else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
             sameStrand = true;
         }
@@ -156,13 +160,29 @@ int main(int argc, char* argv[]) {
         cerr << endl << "*****" << endl << "*****ERROR: Use -scores or -names, not both. " << endl << "*****" << endl;
         showHelp = true;
     }
+    if (useScores && useIntervals) {
+        cerr << endl << "*****" << endl << "*****ERROR: Use -scores or -intervals, not both. " << endl << "*****" << endl;
+        showHelp = true;
+    }
+    if (useNames && useIntervals) {
+        cerr << endl << "*****" << endl << "*****ERROR: Use -names or -intervals, not both. " << endl << "*****" << endl;
+        showHelp = true;
+    }
+    if (!haveLabels && useIntervals) {
+        cerr << endl << "*****" << endl << "*****ERROR: Supply -labels when using -intervals. " << 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, useScores, sameStrand, diffStrand, overlapFraction);
+        TagBam *ba = new TagBam(bamFile, inputFiles, inputLabels, 
+                                tag, useNames, useScores,  
+                                useIntervals, sameStrand, diffStrand, 
+                                overlapFraction);
         ba->Tag();
         delete ba;
         return 0;
@@ -201,9 +221,11 @@ 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;
-    
+    cerr << "\t-scores\t"       << "Use the score field from the annotation files to populate tags." << endl;
+    cerr                        << "\t\tBy default, the -labels values are used." << endl << endl;    
+
+    cerr << "\t-intervals\t"    << "Use the full interval (including name, score, and strand) to populate tags." << endl;
+    cerr                        << "\t\t\tRequires the -labels option to identify from which file the interval came." << endl << endl;    
     
     exit(1);
 }