Merge pull request #119 from tanubrata/master

Added a check function for JaBbA to verify if gGnome has CPLEX added.

DESCRIPTION

@@ -8,11 +8,12 @@ Authors@R:
 Description: The gGnome package provides a flexible, queriable R interface to graphs and walks of reference genomic intervals. gGnome is written in the R6 object oriented standard and built around a powerful GenomicRanges, data.table, and igraph backend, and thus supports agile interaction with graphs consisting of hundreds of thousands of nodes and edges.
 NeedsCompilation: yes
 Remotes: 
-  github::mskilab/gUtils,
-  github::mskilab/gTrack,
-  github::mskilab/fishHook,
-  github::mskilab/bamUtils,
-  github::mskilab/gChain
+  github::mskilab-org/gUtils,
+  github::mskilab-org/gTrack,
+  github::mskilab-org/fishHook,
+  github::mskilab-org/bamUtils,
+  github::mskilab-org/gChain,
+  github::Bioconductor/VariantAnnotation
 Depends:
     R (>= 4.0.0),
     data.table (>= 1.14),
@@ -21,7 +22,7 @@ Depends:
     gTrack,
     gUtils,     
     reshape2,
-    GenomicRanges,
+    GenomicRanges
 Imports:
     methods,
     R6,

NAMESPACE

@@ -25,6 +25,7 @@ S3method(length,gGraph)
 S3method(length,gNode)
 S3method(length,gWalk)
 S3method(merge,Junction)
+S3method(split,gGraph)
 S3method(sum,gGraph)
 S3method(unique,Junction)
 export(Junction)
@@ -36,6 +37,7 @@ export(chromoplexy)
 export(chromothripsis)
 export(cougar2gg)
 export(cov2arrow)
+export(cov2arrowPGV)
 export(cov2cov.js)
 export(cov2csv)
 export(del)
@@ -53,6 +55,7 @@ export(gGraph)
 export(gNode)
 export(gW)
 export(gWalk)
+export(gen_js_cov_PGV)
 export(gen_js_coverage_files)
 export(gen_js_datafiles)
 export(gstat)
@@ -86,7 +89,6 @@ export(refresh)
 export(rel2abs)
 export(setxor)
 export(simple)
-export(split.gGraph)
 export(tic)
 export(transplant)
 exportMethods("%&%")