Merge pull request arq5x#1030 from brentp/genomeCoverageFormat

genomecov: use integer when scale == 1.0

src/genomeCoverageBed/genomeCoverageBed.cpp

@@ -108,7 +108,7 @@ void BedGenomeCoverage::StartNewChrom(const string& newChrom) {
     if (_visitedChromosomes.find(newChrom) != _visitedChromosomes.end()) {
         cerr << "Input error: Chromosome "
              << _currChromName
-             << " found in non-sequential lines. This suggests that the input file is not sorted correctly." 
+             << " found in non-sequential lines. This suggests that the input file is not sorted correctly."
              << endl;
     }
     _visitedChromosomes.insert(newChrom);
@@ -121,9 +121,9 @@ void BedGenomeCoverage::StartNewChrom(const string& newChrom) {
     if (_currChromSize >= 0)
         _currChromCoverage.resize(_currChromSize);
     else {
-        cerr << "Input error: Chromosome " 
-             << _currChromName 
-             << " found in your input file but not in your genome file." 
+        cerr << "Input error: Chromosome "
+             << _currChromName
+             << " found in your input file but not in your genome file."
              << endl;
         exit(1);
     }
@@ -132,7 +132,7 @@ void BedGenomeCoverage::StartNewChrom(const string& newChrom) {
 
 void BedGenomeCoverage::AddCoverage(CHRPOS start, CHRPOS end) {
     // process the first line for this chromosome.
-    // make sure the coordinates fit within the chrom 
+    // make sure the coordinates fit within the chrom
     if (start < _currChromSize)
         _currChromCoverage[start].starts++;
     if (end >= 0 && end < _currChromSize)
@@ -165,16 +165,16 @@ void BedGenomeCoverage::CoverageBed() {
         if (_bed->_status == BED_VALID) {
             if (_filterByStrand == true) {
                 if (a.strand.empty()) {
-                    cerr << "Input error: Interval is missing a strand value on line " 
-                         << _bed->_lineNum 
+                    cerr << "Input error: Interval is missing a strand value on line "
+                         << _bed->_lineNum
                          << "." <<endl;
                     exit(1);
                 }
                 if ( ! (a.strand == "-" || a.strand == "+") ) {
-                    cerr << "Input error: Invalid strand value (" 
-                         << a.strand << ") on line " 
-                         << _bed->_lineNum 
-                         << "." 
+                    cerr << "Input error: Invalid strand value ("
+                         << a.strand << ") on line "
+                         << _bed->_lineNum
+                         << "."
                          << endl;
                     exit(1);
                 }
@@ -258,8 +258,8 @@ void BedGenomeCoverage::CoverageBam(string bamFile) {
     // open the BAM file
     BamReader reader;
     if (!reader.Open(bamFile)) {
-        cerr << "Failed to open BAM file " 
-             << bamFile 
+        cerr << "Failed to open BAM file "
+             << bamFile
              << endl;
         exit(1);
     }
@@ -384,8 +384,11 @@ void BedGenomeCoverage::ReportChromCoverage(const vector<DEPTH> &chromCov, const
 
             depth += chromCov[pos].starts;
             // report the depth for this position.
-            if (depth>0 || !_eachBaseZeroBased)
-                cout << chrom << "\t" << pos+offset << "\t" << depth * _scale << endl;
+            if (depth>0 || !_eachBaseZeroBased) {
+                cout << chrom << "\t" << pos+offset << "\t"
+                     << (_scale == 1.0 ? depth : depth * _scale)
+                     << endl;
+            }
             depth = depth - chromCov[pos].ends;
         }
     }
@@ -488,13 +491,13 @@ void BedGenomeCoverage::ReportChromCoverageBedGraph(const vector<DEPTH> &chromCo
                 if (lastDepth >= _max) {
                     lastDepth = _max;
                 }
-                cout << chrom 
-                     << "\t" 
-                     << lastStart 
-                     << "\t" 
-                     << pos 
-                     << "\t" 
-                     << lastDepth * _scale 
+                cout << chrom
+                     << "\t"
+                     << lastStart
+                     << "\t"
+                     << pos
+                     << "\t"
+                     << (_scale == 1.0 ? lastDepth : lastDepth * _scale)
                      << endl;
             }
             //Set current position as the new interval start + depth
@@ -508,13 +511,13 @@ void BedGenomeCoverage::ReportChromCoverageBedGraph(const vector<DEPTH> &chromCo
     }
     //Print information about the last position
     if ( (lastDepth != -1) && (lastDepth > 0 || _bedGraphAll) ) {
-        cout << chrom 
-             << "\t" 
-             << lastStart 
-             << "\t" 
-             << chromSize 
-             << "\t" 
-             << lastDepth * _scale 
+        cout << chrom
+             << "\t"
+             << lastStart
+             << "\t"
+             << chromSize
+             << "\t"
+             << (_scale == 1.0 ? lastDepth : lastDepth * _scale)
              << endl;
     }
 }