Commit cdc3eea0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added index check

parent 2f23e353
......@@ -63,6 +63,7 @@ object BaseCounter extends ToolCommand {"Start reading RefFlat file")
val bamReader = SamReaderFactory.makeDefault().open(cmdArgs.bamFile)
require(bamReader.hasIndex, "Bamfile require an index")
val geneReader = GeneAnnotationReader.loadRefFlat(cmdArgs.refFlat, bamReader.getFileHeader.getSequenceDictionary)
bamReader.close()"Done reading RefFlat file")
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment