From 7cc6a711b23d9c1ad09b68c37a80f7cc5c90c865 Mon Sep 17 00:00:00 2001 From: Frank Austin Nothaft Date: Mon, 17 Nov 2014 19:55:17 -0800 Subject: [PATCH] [ADAM-486] Add port option to viz command. --- .../src/main/scala/org/bdgenomics/adam/cli/VizReads.scala | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/VizReads.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/VizReads.scala index 35b6fd73f6..c8b001cc70 100644 --- a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/VizReads.scala +++ b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/VizReads.scala @@ -104,6 +104,9 @@ class VizReadsArgs extends Args4jBase with ParquetArgs { @Argument(required = true, metaVar = "REFNAME", usage = "The reference to view", index = 1) var refName: String = null + + @Args4jOption(required = false, name = "-port", usage = "The port to bind to for visualization. The default is 8080.") + var port: Int = 8080 } class VizServlet extends ScalatraServlet with JacksonJsonSupport { @@ -167,12 +170,12 @@ class VizReads(protected val args: VizReadsArgs) extends ADAMSparkCommand[VizRea val proj = Projection(contig, readMapped, readName, start, end) VizReads.reads = sc.loadAlignments(args.inputPath, projection = Some(proj)) - val server = new org.eclipse.jetty.server.Server(8080) + val server = new org.eclipse.jetty.server.Server(args.port) val handlers = new org.eclipse.jetty.server.handler.ContextHandlerCollection() server.setHandler(handlers) handlers.addHandler(new org.eclipse.jetty.webapp.WebAppContext("adam-cli/src/main/webapp", "/")) server.start() - println("View the visualization at: 8080") + println("View the visualization at: " + args.port) println("Frequency visualization at: /freq") println("Overlapping reads visualization at: /reads") server.join()