lineNum is now tracked privately.

src/bed12ToBed6/bed12ToBed6.cpp

@@ -144,7 +144,7 @@ void ProcessBed(istream &bedInput, BedFile *bed) {
         if (bedStatus == BED_VALID) {
 
             bedVector bedBlocks;  // vec to store the discrete BED "blocks" from a
-            splitBedIntoBlocks(bedEntry, lineNum, bedBlocks);
+            splitBedIntoBlocks(bedEntry, bedBlocks);
 
             for (int i = 0; i < (int) bedBlocks.size(); ++i) {
                 if (addBlockNums == false) {

src/coverageBed/coverageBed.cpp

@@ -65,7 +65,7 @@ void BedCoverage::CollectCoverageBed() {
             // split the BED into discrete blocksand process each independently.
             else {
                 bedVector bedBlocks;
-                splitBedIntoBlocks(a, lineNum, bedBlocks);
+                splitBedIntoBlocks(a, bedBlocks);
 
                 // use countSplitHits to avoid over-counting each split chunk
                 // as distinct read coverage.

src/genomeCoverageBed/genomeCoverageBed.cpp

@@ -174,7 +174,7 @@ void BedGenomeCoverage::CoverageBed() {
 
             if (_obeySplits == true) {
                 bedVector bedBlocks; // vec to store the discrete BED "blocks"
-                splitBedIntoBlocks(a, lineNum, bedBlocks);
+                splitBedIntoBlocks(a, bedBlocks);
                 AddBlockedCoverage(bedBlocks);
             }
             else if (_only_5p_end) {

src/multiIntersectBed/multiIntersectBed.cpp

@@ -155,8 +155,7 @@ void MultiIntersectBed::LoadNextItem(int index) {
 
     BedFile *file = input_files[index];
     BED merged_bed;
-    int lineNum = 0;
-    while (file->GetNextMergedBed(merged_bed, lineNum))
+    while (file->GetNextMergedBed(merged_bed))
     {
         current_item[index] = merged_bed;
         break;

src/unionBedGraphs/unionBedGraphs.cpp

@@ -180,7 +180,7 @@ void UnionBedGraphs::LoadNextBedgraphItem(int index) {
         if (status != BEDGRAPH_VALID)
             continue;
 
-        current_bedgraph_item[index] = bg ;
+        current_bedgraph_item[index] = bg;
         break;
     }
 }