diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala
index affbb7b237..dfcb18da9b 100644
--- a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala
+++ b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala
@@ -61,7 +61,6 @@ object ADAMMain extends Logging {
           PrintADAM,
           PrintGenes,
           FlagStat,
-          VizReads,
           PrintTags,
           ListDict,
           AlleleCount,
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
deleted file mode 100644
index edf4bffbf4..0000000000
--- a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/VizReads.scala
+++ /dev/null
@@ -1,230 +0,0 @@
-/**
- * Licensed to Big Data Genomics (BDG) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The BDG licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.bdgenomics.adam.cli
-
-import org.apache.hadoop.mapreduce.Job
-import org.apache.spark.SparkContext
-import org.bdgenomics.adam.models.VariantContext
-import org.apache.spark.rdd.RDD
-import org.bdgenomics.adam.models.{ OrderedTrackedLayout, ReferenceRegion }
-import org.bdgenomics.adam.projections.AlignmentRecordField._
-import org.bdgenomics.adam.projections.Projection
-import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rich.ReferenceMappingContext._
-import org.bdgenomics.formats.avro.{ AlignmentRecord, Genotype, GenotypeAllele }
-import org.fusesource.scalate.TemplateEngine
-import org.json4s._
-import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
-import org.scalatra.json._
-import org.scalatra.ScalatraServlet
-
-object VizReads extends ADAMCommandCompanion {
-  val commandName: String = "viz"
-  val commandDescription: String = "Generates images from sections of the genome"
-
-  var refName = ""
-  var inputPath = ""
-  var reads: RDD[AlignmentRecord] = null
-  var variants: RDD[Genotype] = null
-
-  val trackHeight = 10
-  val width = 1200
-  val height = 400
-  val base = 50
-
-  def apply(cmdLine: Array[String]): ADAMCommand = {
-    new VizReads(Args4j[VizReadsArgs](cmdLine))
-  }
-
-  def printTrackJson(layout: OrderedTrackedLayout[AlignmentRecord]): List[TrackJson] = {
-    var tracks = new scala.collection.mutable.ListBuffer[TrackJson]
-
-    // draws a box for each read, in the appropriate track
-    for ((rec, track) <- layout.trackAssignments) {
-      val aRec = rec.asInstanceOf[AlignmentRecord]
-      tracks += new TrackJson(aRec.getReadName, aRec.getStart, aRec.getEnd, track)
-    }
-    tracks.toList
-  }
-
-  def printVariationJson(layout: OrderedTrackedLayout[Genotype]): List[VariationJson] = {
-    var tracks = new scala.collection.mutable.ListBuffer[VariationJson]
-
-    for ((rec, track) <- layout.trackAssignments) {
-      val aRec = rec.asInstanceOf[Genotype]
-      val referenceAllele = aRec.getVariant.getReferenceAllele
-      val alternateAllele = aRec.getVariant.getAlternateAllele
-      tracks += new VariationJson(aRec.getVariant.getContig.getContigName, aRec.getAlleles.mkString(" / "), aRec.getVariant.getStart, aRec.getVariant.getEnd, track)
-
-    }
-    tracks.toList
-  }
-
-  def printJsonFreq(array: Array[AlignmentRecord], region: ReferenceRegion): List[FreqJson] = {
-    val freqMap = new java.util.TreeMap[Long, Long]
-    var freqBuffer = new scala.collection.mutable.ListBuffer[FreqJson]
-
-    // initiates map with 0 values
-    var i0 = region.start
-    while (i0 <= region.end) {
-      freqMap.put(i0, 0)
-      i0 += 1
-    }
-
-    // creates a point for each base showing its frequency
-    for (rec <- array) {
-      val aRec = rec.asInstanceOf[AlignmentRecord]
-      var i = aRec.getStart
-      while (i <= aRec.getEnd) {
-        if (i >= region.start && i <= region.end)
-          freqMap.put(i, freqMap(i) + 1)
-        i += 1
-      }
-    }
-
-    // convert to list of FreqJsons
-    val iter = freqMap.keySet.iterator
-    var key = 0L
-    while (iter.hasNext) {
-      key = iter.next()
-      freqBuffer += FreqJson(key, freqMap(key))
-    }
-
-    freqBuffer.toList
-  }
-}
-
-case class TrackJson(readName: String, start: Long, end: Long, track: Long)
-case class VariationJson(contigName: String, alleles: String, start: Long, end: Long, track: Long)
-case class FreqJson(base: Long, freq: Long)
-
-class VizReadsArgs extends Args4jBase with ParquetArgs {
-  @Argument(required = true, metaVar = "INPUT", usage = "The ADAM Records file to view", index = 0)
-  var inputPath: String = null
-
-  @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 {
-  protected implicit val jsonFormats: Formats = DefaultFormats
-  var regInfo = ReferenceRegion(VizReads.refName, 0, 200)
-  var filteredLayout: OrderedTrackedLayout[AlignmentRecord] = null
-  var filteredArray: Array[AlignmentRecord] = null
-
-  get("/?") {
-    redirect(url("reads"))
-  }
-
-  get("/reads/?") {
-    contentType = "text/html"
-
-    filteredLayout = new OrderedTrackedLayout(VizReads.reads.filterByOverlappingRegion(regInfo).collect())
-    val templateEngine = new TemplateEngine
-    templateEngine.layout("adam-cli/src/main/webapp/WEB-INF/layouts/reads.ssp",
-      Map("regInfo" -> (regInfo.referenceName, regInfo.start.toString, regInfo.end.toString),
-        "width" -> VizReads.width.toString,
-        "base" -> VizReads.base.toString,
-        "numTracks" -> filteredLayout.numTracks.toString,
-        "trackHeight" -> VizReads.trackHeight.toString))
-  }
-
-  get("/reads/:ref") {
-    contentType = formats("json")
-
-    regInfo = ReferenceRegion(params("ref"), params("start").toLong, params("end").toLong)
-    filteredLayout = new OrderedTrackedLayout(VizReads.reads.filterByOverlappingRegion(regInfo).collect())
-    VizReads.printTrackJson(filteredLayout)
-  }
-
-  get("/freq") {
-    contentType = "text/html"
-
-    filteredArray = VizReads.reads.filterByOverlappingRegion(regInfo).collect()
-    val templateEngine = new TemplateEngine
-    templateEngine.layout("adam-cli/src/main/webapp/WEB-INF/layouts/freq.ssp",
-      Map("regInfo" -> (regInfo.referenceName, regInfo.start.toString, regInfo.end.toString),
-        "width" -> VizReads.width.toString,
-        "height" -> VizReads.height.toString,
-        "base" -> VizReads.base.toString))
-  }
-
-  get("/freq/:ref") {
-    contentType = formats("json")
-
-    regInfo = ReferenceRegion(params("ref"), params("start").toLong, params("end").toLong)
-    filteredArray = VizReads.reads.filterByOverlappingRegion(regInfo).collect()
-    VizReads.printJsonFreq(filteredArray, regInfo)
-  }
-
-  get("/variants/?") {
-    contentType = "text/html"
-
-    val input = VizReads.variants.filterByOverlappingRegion(regInfo).collect()
-    val filteredGenotypeTrack = new OrderedTrackedLayout(input)
-    val templateEngine = new TemplateEngine
-    val displayMap = Map("regInfo" -> (regInfo.referenceName, regInfo.start.toString, regInfo.end.toString),
-      "width" -> VizReads.width.toString,
-      "base" -> VizReads.base.toString,
-      "numTracks" -> filteredGenotypeTrack.numTracks.toString,
-      "trackHeight" -> VizReads.trackHeight.toString)
-    templateEngine.layout("adam-cli/src/main/webapp/WEB-INF/layouts/variants.ssp",
-      displayMap)
-  }
-
-  get("/variants/:ref") {
-    contentType = formats("json")
-
-    regInfo = ReferenceRegion(params("ref"), params("start").toLong, params("end").toLong)
-    val input = VizReads.variants.filterByOverlappingRegion(regInfo).collect()
-    val filteredGenotypeTrack = new OrderedTrackedLayout(input)
-    VizReads.printVariationJson(filteredGenotypeTrack)
-  }
-}
-
-class VizReads(protected val args: VizReadsArgs) extends ADAMSparkCommand[VizReadsArgs] {
-  val companion: ADAMCommandCompanion = VizReads
-
-  def run(sc: SparkContext, job: Job): Unit = {
-    VizReads.refName = args.refName
-
-    val proj = Projection(contig, readMapped, readName, start, end)
-
-    if (args.inputPath.endsWith(".bam") || args.inputPath.endsWith(".sam") || args.inputPath.endsWith(".align.adam")) {
-      VizReads.reads = sc.loadAlignments(args.inputPath, projection = Some(proj))
-    }
-
-    if (args.inputPath.endsWith(".vcf") || args.inputPath.endsWith(".gt.adam")) {
-      VizReads.variants = sc.loadGenotypes(args.inputPath, projection = Some(proj))
-    }
-
-    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: " + args.port)
-    println("Frequency visualization at: /freq")
-    println("Overlapping reads visualization at: /reads")
-    println("Variant visualization at: /variants")
-    server.join()
-  }
-}
diff --git a/adam-cli/src/main/webapp/WEB-INF/layouts/freq.ssp b/adam-cli/src/main/webapp/WEB-INF/layouts/freq.ssp
deleted file mode 100644
index ca7a3cf731..0000000000
--- a/adam-cli/src/main/webapp/WEB-INF/layouts/freq.ssp
+++ /dev/null
@@ -1,359 +0,0 @@
-<%@ val regInfo: (String, String, String) %>
-<%@ val width: String %>
-<%@ val height: String %>
-<%@ val base: String %>
-
-<html>
-<head lang="en">
-    <meta charset="UTF-8">
-    <script src="http://d3js.org/d3.v3.min.js" charset="utf-8"></script>
-    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
-    <link href='http://fonts.googleapis.com/css?family=Open+Sans:300,400,600,700' rel='stylesheet' type='text/css'>
-    <style>
-        body {
-            background: whitesmoke;
-            font-family: 'Open Sans', sans-serif;
-            font-weight:300;
-        }
-        h1 {
-            text-align: center;
-            margin: 10px 0 0 0;
-            color: #333333;
-            font-weight:400;
-            text-transform: uppercase;
-        }
-        .highlight {
-            font-weight:700;
-        }
-	    h2 {
-	        text-align: center;
-	        margin: 0 0 10px 0;
-	        color: #999999;
-	        font-weight:300;
-	    }
-	    ul {
-            list-style-type: none;
-            margin: 0;
-            padding: 0 5px 0 5px;
-            float: left;
-        }
-        li {
-            display: inline;
-            float: left;
-            padding: 0 0 0 5px;
-        }
-        .axis path,
-        .axis line {
-            fill: none;
-            stroke: black;
-            shape-rendering: crispEdges;
-        }
-        .axis text {
-            font-family: sans-serif;
-            font-size: 11px;
-        }
-        input[type="text"] {
-            height: 22px;
-        }
-    </style>
-    <title>Genome visualization for ADAM</title>
-</head>
-<body>
-    <h1>Genome visualization for <span class='highlight'>ADAM</span></h1>
-    <h2 align="center">current region: ${regInfo._1}:</h2>
-    <br>
-    <ul>
-        <li>move:</li>
-        <li>
-            <input name="Move very far left button"
-               type="button"
-               value="<<<"
-               onclick="moveVeryFarLeft()"
-               class="btn btn-primary btn-xs"/>
-        </li>
-        <li>
-            <input name="Move far left button"
-               type="button"
-               value="<<"
-               onclick="moveFarLeft()"
-               class="btn btn-primary btn-xs"/>
-        </li>
-        <li>
-            <input name="Move left button"
-               type="button"
-               value="<"
-               onclick="moveLeft()"
-               class="btn btn-primary btn-xs"/>
-        </li>
-        <li>
-            <input name="Move right button"
-               type="button"
-               value=">"
-               onclick="moveRight()"
-               class="btn btn-info btn-xs"/>
-        </li>
-        <li>
-            <input name="Move far right button"
-               type="button"
-               value=">>"
-               onclick="moveFarRight()"
-               class="btn btn-info btn-xs"/>
-        </li>
-        <li>
-            <input name="Move very far right button"
-               type="button"
-               value=">>>"
-               onclick="moveVeryFarRight()"
-               class="btn btn-info btn-xs"/>
-        </li>
-        <li>zoom:</li>
-        <li>
-            <input name="Zoom in button"
-               type="button"
-               value="++"
-               onclick="zoomIn()"
-               class="btn btn-warning btn-xs"/>
-        </li>
-        <li>
-            <input name="Zoom out button"
-               type="button"
-               value="--"
-               onclick="zoomOut()"
-               class="btn btn-warning btn-xs"/>
-        </li>
-        <li>
-            <form name="regForm" method="GET" class="form-inline">
-                region:
-                <input type="text" name="start" size="10" class="form-control" placeholder="start">
-                - <input type="text" name="end" size="10" class="form-control" placeholder="end">
-                <input name="Submit button"
-                       type="button"
-                       value="Submit"
-                       onclick="checkForm(this.form)"
-                       class="btn btn-danger btn-xs"/>
-            </form>
-        </li>
-    </ul>
-    <br>
-    <script>
-        var refName = "${regInfo._1}";
-        var start = parseInt(${regInfo._2}, 10);
-        var end = parseInt(${regInfo._3}, 10);
-        var width = parseInt(${width}, 10);
-        var base = parseInt(${base}, 10);
-        var height = ${height};
-        var maxFreq = 0;
-        var jsonLocation = "/freq/" + refName + "?start=" + start + "&end=" + end;
-
-        d3.select("h2")
-          .append("span")
-          .text(start + "-" + end);
-
-        d3.json(jsonLocation, function(error, data) {
-            data.forEach(function(d) {
-                d.base = +d.base;
-                d.freq = +d.freq;
-                if (d.freq > maxFreq) { maxFreq = d.freq; }
-            });
-
-            var svgContainer = d3.select("body")
-                                 .append("svg")
-                                 .attr("height", (height+base))
-                                 .attr("width", (width+base));
-
-            // Create the scale for the data
-            var dataScale = d3.scale.linear()
-                                    .domain([0, maxFreq])
-                                    .range([0, height]);
-
-            var freqline = d3.svg.line()
-                             .x(function(d){return base + (d.base-start)/(end-start) * width;})
-                             .y(function(d){return dataScale(maxFreq-d.freq);})
-                             .interpolate("basis");
-
-            svgContainer.append("g")
-                        .append("svg:path")
-                        .attr("d", freqline(data))
-                        .style("stroke-width", 2)
-                        .style("stroke", "steelblue")
-                        .style("fill", "none");
-
-            // Create the scale for the x axis
-            var xAxisScale = d3.scale.linear()
-                                    .domain([start, end])
-                                    .range([0, width]);
-
-            // Create the scale for the y axis
-            var yAxisScale = d3.scale.linear()
-                                    .domain([maxFreq, 0])
-                                    .range([0, height]);
-
-            // Create the x axis
-            var xAxis = d3.svg.axis()
-                           .scale(xAxisScale)
-                           .ticks(5);
-
-            // Create the y axis
-            var yAxis = d3.svg.axis()
-                           .scale(yAxisScale)
-                           .orient("left")
-                           .ticks(5);
-
-            // Add the x axis to the container
-            svgContainer.append("g")
-                        .attr("class", "axis")
-                        .attr("transform", "translate(" + base + ", " + height + ")")
-                        .call(xAxis);
-
-            // Add the y axis to the container
-            svgContainer.append("g")
-                        .attr("class", "axis")
-                        .attr("transform", "translate(" + base + ", 0)")
-                        .call(yAxis);
-        });
-
-        // Try to move very far left
-        function moveVeryFarLeft() {
-            var newStart = Math.max(0, start - (end-start));
-            var newEnd = Math.max(newStart, end - (end-start));
-            update(newStart, newEnd);
-        }
-
-        // Try to move far left
-        function moveFarLeft() {
-            var newStart = Math.max(0, start - (end-start)/2);
-            var newEnd = Math.max(newStart, end - (end-start)/2);
-            update(newStart, newEnd);
-        }
-
-        // Try to move left
-        function moveLeft() {
-            var newStart = Math.max(0, start - (end-start)/4);
-            var newEnd = Math.max(newStart, end - (end-start)/4);
-            update(newStart, newEnd);
-        }
-
-         // Try to move right
-         function moveRight() {
-             var newStart = start + (end-start)/4;
-             var newEnd = end + (end-start)/4;
-             update(newStart, newEnd);
-         }
-
-        // Try to move far right
-        function moveFarRight() {
-            var newStart = start + (end-start)/2;
-            var newEnd = end + (end-start)/2;
-            update(newStart, newEnd);
-        }
-
-        // Try to move very far right
-        function moveVeryFarRight() {
-            var newStart = start + (end-start);
-            var newEnd = end + (end-start);
-            update(newStart, newEnd);
-        }
-
-        // Try to zoom in
-        function zoomIn() {
-            var newStart = start + (end-start)/4;
-            var newEnd = end - (end-start)/4;
-            update(newStart, newEnd);
-        }
-
-        // Try to zoom out
-        function zoomOut() {
-            var newStart = Math.max(0, start - (end-start)/2);
-            var newEnd = end - (end-start)/2;
-            update(newStart, newEnd);
-        }
-
-        // Redirect based on form input
-        function checkForm(form) {
-            var newStart = Math.max(0, form.start.value);
-            var newEnd = Math.max(newStart, form.end.value);
-            form.reset();
-            update(newStart, newEnd);
-        }
-
-        function update(newStart, newEnd) {
-            start = newStart;
-            end = newEnd;
-            jsonLocation = ("/freq/" + refName + "?start=" + start + "&end=" + end);
-            maxFreq = 0;
-
-            d3.json(jsonLocation, function(error, data) {
-                data.forEach(function(d) {
-                    d.base = +d.base;
-                    d.freq = +d.freq;
-                    if (d.freq > maxFreq) { maxFreq = d.freq; }
-                });
-
-                d3.select("h2")
-                              .select("span")
-                              .text(start + "-" + end);
-
-
-                // Create the scale for the data
-                var dataScale = d3.scale.linear()
-                                        .domain([0, maxFreq])
-                                        .range([0, height]);
-
-                var freqline = d3.svg.line()
-                                 .x(function(d){return base + (d.base-start)/(end-start) * width;})
-                                 .y(function(d){return dataScale(maxFreq-d.freq);})
-                                 .interpolate("basis");
-
-                // Change dimensions of the SVG container
-                var svgContainer = d3.select("svg")
-                                     .attr("height", (height+base));
-
-                // Remove old content
-                svgContainer.selectAll("g")
-                            .remove();
-
-                // Add the path
-                svgContainer.append("g")
-                            .append("path")
-                            .attr("d", freqline(data))
-                            .style("stroke-width", 2)
-                            .style("stroke", "steelblue")
-                            .style("fill", "none");
-
-                // Create the scale for the x axis
-                var xAxisScale = d3.scale.linear()
-                                        .domain([start, end])
-                                        .range([0, width]);
-
-                // Create the scale for the y axis
-                var yAxisScale = d3.scale.linear()
-                                        .domain([maxFreq, 0])
-                                        .range([0, height]);
-
-                // Create the x axis
-                var xAxis = d3.svg.axis()
-                               .scale(xAxisScale)
-                               .ticks(5);
-
-                // Create the y axis
-                var yAxis = d3.svg.axis()
-                               .scale(yAxisScale)
-                               .orient("left")
-                               .ticks(5);
-
-                // Add the x axis to the container
-                svgContainer.append("g")
-                            .attr("class", "axis")
-                            .attr("transform", "translate(" + base + ", " + height + ")")
-                            .call(xAxis);
-
-                // Add the y axis to the container
-                svgContainer.append("g")
-                            .attr("class", "axis")
-                            .attr("transform", "translate(" + base + ", 0)")
-                            .call(yAxis);
-            });
-        }
-    </script>
-</body>
-</html>
\ No newline at end of file
diff --git a/adam-cli/src/main/webapp/WEB-INF/layouts/reads.ssp b/adam-cli/src/main/webapp/WEB-INF/layouts/reads.ssp
deleted file mode 100644
index a02d1f47eb..0000000000
--- a/adam-cli/src/main/webapp/WEB-INF/layouts/reads.ssp
+++ /dev/null
@@ -1,360 +0,0 @@
-<%@ val regInfo: (String, String, String) %>
-<%@ val width: String %>
-<%@ val base: String %>
-<%@ val trackHeight: String %>
-<%@ val numTracks: String %>
-
-<html>
-<head lang="en">
-    <meta charset="UTF-8">
-    <script src="http://d3js.org/d3.v3.min.js" charset="utf-8"></script>
-    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
-    <link href='http://fonts.googleapis.com/css?family=Open+Sans:300,400,600,700' rel='stylesheet' type='text/css'>
-    <style>
-        body {
-            background: whitesmoke;
-            font-family: 'Open Sans', sans-serif;
-            font-weight:300;
-        }
-        h1 {
-            text-align: center;
-            margin: 10px 0 0 0;
-            color: #333333;
-            font-weight:400;
-            text-transform: uppercase;
-        }
-        .highlight {
-            font-weight:700;
-        }
-        h2 {
-            text-align: center;
-            margin: 0 0 10px 0;
-            color: #999999;
-            font-weight:300;
-        }
-        ul {
-            list-style-type: none;
-            margin: 0;
-            padding: 0 5px 0 5px;
-            float: left;
-        }
-        li {
-            display: inline;
-            float: left;
-            padding: 0 0 0 5px;
-        }
-        .axis path,
-        .axis line {
-            fill: none;
-            stroke: black;
-            shape-rendering: crispEdges;
-        }
-        .axis text {
-            font-family: sans-serif;
-            font-size: 11px;
-        }
-        div.tooltip {
-            position: absolute;
-            text-align: center;
-            padding: 2px;
-            background: lightsteelblue;
-            border: 0px;
-            pointer-events: none;
-        }
-        rect {
-            fill: slategray;
-        }
-        input[type="text"] {
-            height: 22px;
-        }
-    </style>
-    <title>Genome visualization for ADAM</title>
-</head>
-<body>
-    <h1>Genome visualization for <span class='highlight'>ADAM</span></h1>
-    <h2 align="center">current region: ${regInfo._1}:</h2>
-    <br>
-    <ul>
-        <li>move:</li>
-        <li>
-            <input name="Move very far left button"
-               type="button"
-               value="<<<"
-               onclick="moveVeryFarLeft()"
-               class="btn btn-primary btn-xs"/>
-        </li>
-        <li>
-            <input name="Move far left button"
-               type="button"
-               value="<<"
-               onclick="moveFarLeft()"
-               class="btn btn-primary btn-xs"/>
-        </li>
-        <li>
-            <input name="Move left button"
-               type="button"
-               value="<"
-               onclick="moveLeft()"
-               class="btn btn-primary btn-xs"/>
-        </li>
-        <li>
-            <input name="Move right button"
-               type="button"
-               value=">"
-               onclick="moveRight()"
-               class="btn btn-info btn-xs"/>
-        </li>
-        <li>
-            <input name="Move far right button"
-               type="button"
-               value=">>"
-               onclick="moveFarRight()"
-               class="btn btn-info btn-xs"/>
-        </li>
-        <li>
-            <input name="Move very far right button"
-               type="button"
-               value=">>>"
-               onclick="moveVeryFarRight()"
-               class="btn btn-info btn-xs"/>
-        </li>
-        <li>zoom:</li>
-        <li>
-            <input name="Zoom in button"
-               type="button"
-               value="++"
-               onclick="zoomIn()"
-               class="btn btn-warning btn-xs"/>
-        </li>
-        <li>
-            <input name="Zoom out button"
-               type="button"
-               value="--"
-               onclick="zoomOut()"
-               class="btn btn-warning btn-xs"/>
-        </li>
-        <li>
-            <form name="regForm" method="GET" class="form-inline">
-                region:
-                <input type="text" name="start" size="10" class="form-control" placeholder="start">
-                - <input type="text" name="end" size="10" class="form-control" placeholder="end">
-                <input name="Submit button"
-                       type="button"
-                       value="Submit"
-                       onclick="checkForm(this.form)"
-                       class="btn btn-danger btn-xs"/>
-            </form>
-        </li>
-    </ul>
-    <br>
-    <script>
-        var refName = "${regInfo._1}";
-        var start = parseInt(${regInfo._2}, 10);
-        var end = parseInt(${regInfo._3}, 10);
-        var width = parseInt(${width}, 10);
-        var base = parseInt(${base}, 10);
-        var trackHeight = parseInt(${trackHeight}, 10);
-        var numTracks = parseInt(${numTracks}, 10);
-        var height = (numTracks+1) * trackHeight;
-        var jsonLocation = "/reads/" + refName + "?start=" + start + "&end=" + end;
-
-        var svgContainer = d3.select("body")
-                             .append("svg")
-                             .attr("height", (height+base))
-                             .attr("width", width);
-
-        d3.select("h2")
-          .append("span")
-          .text(start + "-" + end);
-
-        d3.json(jsonLocation, function(error, data) {
-            data.forEach(function(d) {
-                d.readName = d.readName;
-                d.start = +d.start;
-                d.end = +d.end;
-                d.track = +d.track;
-            });
-
-            // Add the rectangles
-            svgContainer.append("g")
-                        .selectAll("rect")
-                        .data(data)
-                        .enter()
-                        .append("rect")
-                        .attr("x", (function(d) { return (d.start-start)/(end-start) * width; }))
-                        .attr("y", (function(d) { return height - trackHeight * (d.track+1); }))
-                        .attr("width", (function(d) { return Math.max(1,(d.end-d.start)*(width/(end-start))); }))
-                        .attr("height", (trackHeight-2))
-                        .on("mouseover", function(d) {
-                                            div.transition()
-                                            .duration(200)
-                                            .style("opacity", .9);
-                                            div .html(d.readName)
-                                            .style("left", (d3.event.pageX) + "px")
-                                            .style("top", (d3.event.pageY - 28) + "px");
-                                        })
-                        .on("mouseout", function(d) {
-                                            div.transition()
-                                            .duration(500)
-                                            .style("opacity", 0);
-                                        });
-        });
-
-        // Create the scale for the axis
-        var axisScale = d3.scale.linear()
-                                .domain([start, end])
-                                .range([0, width]);
-
-        // Create the axis
-        var xAxis = d3.svg.axis()
-                       .scale(axisScale)
-                       .ticks(5);
-
-        // Add the axis to the container
-        svgContainer.append("g")
-                    .attr("class", "axis")
-                    .attr("transform", "translate(0, " + height + ")")
-                    .call(xAxis);
-
-        // Try to move very far left
-        function moveVeryFarLeft() {
-            var newStart = Math.max(0, start - (end-start));
-            var newEnd = Math.max(newStart, end - (end-start));
-            update(newStart, newEnd);
-        }
-
-        // Try to move far left
-        function moveFarLeft() {
-            var newStart = Math.max(0, start - (end-start)/2);
-            var newEnd = Math.max(newStart, end - (end-start)/2);
-            update(newStart, newEnd);
-        }
-
-        // Try to move left
-        function moveLeft() {
-            var newStart = Math.max(0, start - (end-start)/4);
-            var newEnd = Math.max(newStart, end - (end-start)/4);
-            update(newStart, newEnd);
-        }
-
-         // Try to move right
-         function moveRight() {
-             var newStart = start + (end-start)/4;
-             var newEnd = end + (end-start)/4;
-             update(newStart, newEnd);
-         }
-
-        // Try to move far right
-        function moveFarRight() {
-            var newStart = start + (end-start)/2;
-            var newEnd = end + (end-start)/2;
-            update(newStart, newEnd);
-        }
-
-        // Try to move very far right
-        function moveVeryFarRight() {
-            var newStart = start + (end-start);
-            var newEnd = end + (end-start);
-            update(newStart, newEnd);
-        }
-
-        // Try to zoom in
-        function zoomIn() {
-            var newStart = start + (end-start)/4;
-            var newEnd = end - (end-start)/4;
-            update(newStart, newEnd);
-        }
-
-        // Try to zoom out
-        function zoomOut() {
-            var newStart = Math.max(0, start - (end-start)/2);
-            var newEnd = end - (end-start)/2;
-            update(newStart, newEnd);
-        }
-
-        // Redirect based on form input
-        function checkForm(form) {
-            var newStart = Math.max(0, form.start.value);
-            var newEnd = Math.max(newStart, form.end.value);
-            form.reset();
-            update(newStart, newEnd);
-        }
-
-        function update(newStart, newEnd) {
-            start = newStart;
-            end = newEnd;
-            jsonLocation = ("/reads/" + refName + "?start=" + start + "&end=" + end);
-            var numTracks = 0;
-
-            d3.json(jsonLocation, function(error, data) {
-                data.forEach(function(d) {
-                    d.readName = d.readName;
-                    d.start = +d.start;
-                    d.end = +d.end;
-                    if (d.track > numTracks) { numTracks = d.track; }
-                });
-
-                d3.select("h2")
-                  .select("span")
-                  .text(start + "-" + end);
-
-                height = (numTracks+1) * trackHeight;
-
-                // Change dimensions of the SVG container
-                var svgContainer = d3.select("svg")
-                                     .attr("height", (height+base));
-
-                // Remove old content
-                svgContainer.selectAll("g")
-                            .remove();
-
-                // Add the rectangles
-                svgContainer.append("g")
-                            .selectAll("rect")
-                            .data(data)
-                            .enter()
-                            .append("rect")
-                            .attr("x", (function(d) { return (d.start-start)/(end-start) * width; }))
-                            .attr("y", (function(d) { return height - trackHeight * (d.track+1); }))
-                            .attr("width", (function(d) { return Math.max(1,(d.end-d.start)*(width/(end-start))); }))
-                            .attr("height", (trackHeight-2))
-                            .on("mouseover", function(d) {
-                                                div.transition()
-                                                .duration(200)
-                                                .style("opacity", .9);
-                                                div .html(d.readName)
-                                                .style("left", (d3.event.pageX) + "px")
-                                                .style("top", (d3.event.pageY - 28) + "px");
-                                            })
-                            .on("mouseout", function(d) {
-                                                div.transition()
-                                                .duration(500)
-                                                .style("opacity", 0);
-                                            });
-
-                // Recreate the scale for the axis
-                var axisScale = d3.scale.linear()
-                                        .domain([start, end])
-                                        .range([0, width]);
-
-                // Recreate the axis
-                var xAxis = d3.svg.axis()
-                               .scale(axisScale)
-                               .ticks(5);
-
-                // Add the axis to the container
-                svgContainer.append("g")
-                            .attr("class", "axis")
-                            .attr("transform", "translate(0, " + height + ")")
-                            .call(xAxis);
-            });
-        }
-
-        // Hover box for reads
-        var div = d3.select("body")
-                    .append("div")
-                    .attr("class", "tooltip")
-                    .style("opacity", 0);
-    </script>
-</body>
-</html>
\ No newline at end of file
diff --git a/adam-cli/src/main/webapp/WEB-INF/layouts/variants.ssp b/adam-cli/src/main/webapp/WEB-INF/layouts/variants.ssp
deleted file mode 100644
index 1c77157291..0000000000
--- a/adam-cli/src/main/webapp/WEB-INF/layouts/variants.ssp
+++ /dev/null
@@ -1,366 +0,0 @@
-<%@ val regInfo: (String, String, String) %>
-<%@ val width: String %>
-<%@ val base: String %>
-<%@ val trackHeight: String %>
-<%@ val numTracks: String %>
-
-<html>
-<head lang="en">
-    <meta charset="UTF-8">
-    <script src="http://d3js.org/d3.v3.min.js" charset="utf-8"></script>
-    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
-    <link href='http://fonts.googleapis.com/css?family=Open+Sans:300,400,600,700' rel='stylesheet' type='text/css'>
-    <style>
-        body {
-            background: whitesmoke;
-            font-family: 'Open Sans', sans-serif;
-            font-weight:300;
-        }
-        h1 {
-            text-align: center;
-            margin: 10px 0 0 0;
-            color: #333333;
-            font-weight:400;
-            text-transform: uppercase;
-        }
-        .highlight {
-            font-weight:700;
-        }
-	    h2 {
-	        text-align: center;
-	        margin: 0 0 10px 0;
-	        color: #999999;
-	        font-weight:300;
-	    }
-	    ul {
-            list-style-type: none;
-            margin: 0;
-            padding: 0 5px 0 5px;
-            float: left;
-        }
-        li {
-            display: inline;
-            float: left;
-            padding: 0 0 0 5px;
-        }
-        .axis path,
-        .axis line {
-            fill: none;
-            stroke: black;
-            shape-rendering: crispEdges;
-        }
-        .axis text {
-            font-family: sans-serif;
-            font-size: 11px;
-        }
-        div.tooltip {
-            position: absolute;
-            text-align: center;
-            padding: 2px;
-            background: lightsteelblue;
-            border: 0px;
-            pointer-events: none;
-        }
-        rect {
-            fill: red;
-        }
-        altrect {
-            fill: slategrey;
-        }
-        input[type="text"] {
-            height: 22px;
-        }
-    </style>
-    <title>Genome visualization for ADAM</title>
-</head>
-<body>
-    <h1>Genome visualization for <span class='highlight'>ADAM</span></h1>
-    <h2 align="center">current region: ${regInfo._1}:</h2>
-    <br>
-    <ul>
-        <li>move:</li>
-        <li>
-            <input name="Move very far left button"
-               type="button"
-               value="<<<"
-               onclick="moveVeryFarLeft()"
-               class="btn btn-primary btn-xs"/>
-        </li>
-        <li>
-            <input name="Move far left button"
-               type="button"
-               value="<<"
-               onclick="moveFarLeft()"
-               class="btn btn-primary btn-xs"/>
-        </li>
-        <li>
-            <input name="Move left button"
-               type="button"
-               value="<"
-               onclick="moveLeft()"
-               class="btn btn-primary btn-xs"/>
-        </li>
-        <li>
-            <input name="Move right button"
-               type="button"
-               value=">"
-               onclick="moveRight()"
-               class="btn btn-info btn-xs"/>
-        </li>
-        <li>
-            <input name="Move far right button"
-               type="button"
-               value=">>"
-               onclick="moveFarRight()"
-               class="btn btn-info btn-xs"/>
-        </li>
-        <li>
-            <input name="Move very far right button"
-               type="button"
-               value=">>>"
-               onclick="moveVeryFarRight()"
-               class="btn btn-info btn-xs"/>
-        </li>
-        <li>zoom:</li>
-        <li>
-            <input name="Zoom in button"
-               type="button"
-               value="++"
-               onclick="zoomIn()"
-               class="btn btn-warning btn-xs"/>
-        </li>
-        <li>
-            <input name="Zoom out button"
-               type="button"
-               value="--"
-               onclick="zoomOut()"
-               class="btn btn-warning btn-xs"/>
-        </li>
-        <li>
-            <form name="regForm" method="GET" class="form-inline">
-                region:
-                <input type="text" name="start" size="10" class="form-control" placeholder="start">
-                - <input type="text" name="end" size="10" class="form-control" placeholder="end">
-                <input name="Submit button"
-                       type="button"
-                       value="Submit"
-                       onclick="checkForm(this.form)"
-                       class="btn btn-danger btn-xs"/>
-            </form>
-        </li>
-    </ul>
-    <br>
-    <script>
-        var refName = "${regInfo._1}";
-        var start = parseInt(${regInfo._2}, 10);
-        var end = parseInt(${regInfo._3}, 10);
-        var width = parseInt(${width}, 10);
-        var base = parseInt(${base}, 10);
-        var trackHeight = parseInt(${trackHeight}, 10);
-        var numTracks = parseInt(${numTracks}, 10);
-        var height = (numTracks+1) * trackHeight;
-        var jsonLocation = "/variants/" + refName + "?start=" + start + "&end=" + end;
-
-        var svgContainer = d3.select("body")
-                             .append("svg")
-                             .attr("height", (height+base))
-                             .attr("width", width);
-
-        d3.select("h2")
-          .append("span")
-          .text(start + "-" + end);
-
-        d3.json(jsonLocation, function(error, data) {
-            data.forEach(function(d) {
-                d.contigName = d.contigName;
-                d.start = +d.start;
-                d.end = +d.end;
-                d.track = +d.track;
-                d.alleles = d.alleles;
-                
-            });
-
-            // Add the rectangles
-            svgContainer.append("g")
-                        .selectAll("rect")
-                        .data(data)
-                        .enter()
-                        .append("rect")
-                        .attr("x", (function(d) { return (d.start-start)/(end-start) * width; }))
-                        .attr("y", (function(d) { return height - trackHeight * (d.track+1); }))
-                        .attr("width", (function(d) { return Math.max(1,(d.end-d.start)*(width/(end-start))); }))
-                        .attr("height", (trackHeight-2))
-                        .on("mouseover", function(d) {
-                                            div.transition()
-                                            .duration(200)
-                                            .style("opacity", .9);
-                                            div .html(d.alleles)
-                                            .style("left", (d3.event.pageX) + "px")
-                                            .style("top", (d3.event.pageY - 28) + "px");
-                                        })
-                        .on("mouseout", function(d) {
-                                            div.transition()
-                                            .duration(500)
-                                            .style("opacity", 0);
-                                        });
-        });
-
-        // Create the scale for the axis
-        var axisScale = d3.scale.linear()
-                                .domain([start, end])
-                                .range([0, width]);
-
-        // Create the axis
-        var xAxis = d3.svg.axis()
-                       .scale(axisScale)
-                       .ticks(5);
-
-        // Add the axis to the container
-        svgContainer.append("g")
-                    .attr("class", "axis")
-                    .attr("transform", "translate(0, " + height + ")")
-                    .call(xAxis);
-
-        // Try to move very far left
-        function moveVeryFarLeft() {
-            var newStart = Math.max(0, start - (end-start));
-            var newEnd = Math.max(newStart, end - (end-start));
-            update(newStart, newEnd);
-        }
-
-        // Try to move far left
-        function moveFarLeft() {
-            var newStart = Math.max(0, start - (end-start)/2);
-            var newEnd = Math.max(newStart, end - (end-start)/2);
-            update(newStart, newEnd);
-        }
-
-        // Try to move left
-        function moveLeft() {
-            var newStart = Math.max(0, start - (end-start)/4);
-            var newEnd = Math.max(newStart, end - (end-start)/4);
-            update(newStart, newEnd);
-        }
-
-         // Try to move right
-         function moveRight() {
-             var newStart = start + (end-start)/4;
-             var newEnd = end + (end-start)/4;
-             update(newStart, newEnd);
-         }
-
-        // Try to move far right
-        function moveFarRight() {
-            var newStart = start + (end-start)/2;
-            var newEnd = end + (end-start)/2;
-            update(newStart, newEnd);
-        }
-
-        // Try to move very far right
-        function moveVeryFarRight() {
-            var newStart = start + (end-start);
-            var newEnd = end + (end-start);
-            update(newStart, newEnd);
-        }
-
-        // Try to zoom in
-        function zoomIn() {
-            var newStart = start + (end-start)/4;
-            var newEnd = end - (end-start)/4;
-            update(newStart, newEnd);
-        }
-
-        // Try to zoom out
-        function zoomOut() {
-            var newStart = Math.max(0, start - (end-start)/2);
-            var newEnd = end - (end-start)/2;
-            update(newStart, newEnd);
-        }
-
-        // Redirect based on form input
-        function checkForm(form) {
-            var newStart = Math.max(0, form.start.value);
-            var newEnd = Math.max(newStart, form.end.value);
-            form.reset();
-            update(newStart, newEnd);
-        }
-
-        function update(newStart, newEnd) {
-            start = newStart;
-            end = newEnd;
-            jsonLocation = ("/variants/" + refName + "?start=" + start + "&end=" + end);
-            var numTracks = 0;
-
-            d3.json(jsonLocation, function(error, data) {
-                data.forEach(function(d) {
-                    d.readName = d.readName;
-                    d.start = +d.start;
-                    d.end = +d.end;
-                    d.alleles = d.alleles;
-                    if (d.track > numTracks) { numTracks = d.track; }
-                });
-
-                d3.select("h2")
-                  .select("span")
-                  .text(start + "-" + end);
-
-                height = (numTracks+1) * trackHeight;
-
-                // Change dimensions of the SVG container
-                var svgContainer = d3.select("svg")
-                                     .attr("height", (height+base));
-
-                // Remove old content
-                svgContainer.selectAll("g")
-                            .remove();
-
-                // Add the rectangles
-                svgContainer.append("g")
-                            .selectAll("rect")
-                            .data(data)
-                            .enter()
-                            .append("rect")
-                            .attr("x", (function(d) { return (d.start-start)/(end-start) * width; }))
-                            .attr("y", (function(d) { return height - trackHeight * (d.track+1); }))
-                            .attr("width", (function(d) { return Math.max(1,(d.end-d.start)*(width/(end-start))); }))
-                            .attr("height", (trackHeight-2))
-                            .on("mouseover", function(d) {
-                                                div.transition()
-                                                .duration(200)
-                                                .style("opacity", .9);
-                                                div .html(d.alleles)
-                                                .style("left", (d3.event.pageX) + "px")
-                                                .style("top", (d3.event.pageY - 28) + "px");
-                                            })
-                            .on("mouseout", function(d) {
-                                                div.transition()
-                                                .duration(500)
-                                                .style("opacity", 0);
-                                            });
-
-                // Recreate the scale for the axis
-                var axisScale = d3.scale.linear()
-                                        .domain([start, end])
-                                        .range([0, width]);
-
-                // Recreate the axis
-                var xAxis = d3.svg.axis()
-                               .scale(axisScale)
-                               .ticks(5);
-
-                // Add the axis to the container
-                svgContainer.append("g")
-                            .attr("class", "axis")
-                            .attr("transform", "translate(0, " + height + ")")
-                            .call(xAxis);
-            });
-        }
-
-        // Hover box for reads
-        var div = d3.select("body")
-                    .append("div")
-                    .attr("class", "tooltip")
-                    .style("opacity", 0);
-    </script>
-</body>
-</html>
diff --git a/adam-cli/src/main/webapp/WEB-INF/web.xml b/adam-cli/src/main/webapp/WEB-INF/web.xml
deleted file mode 100644
index 0f1124996b..0000000000
--- a/adam-cli/src/main/webapp/WEB-INF/web.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<web-app version="2.5" xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd">
-    <servlet>
-        <servlet-name>adam</servlet-name>
-        <servlet-class>org.bdgenomics.adam.cli.VizServlet</servlet-class>
-    </servlet>
-    <servlet-mapping>
-        <servlet-name>adam</servlet-name>
-        <url-pattern>/*</url-pattern>
-    </servlet-mapping>
-</web-app>
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/TrackedLayout.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/TrackedLayout.scala
deleted file mode 100644
index 654ddb01c3..0000000000
--- a/adam-core/src/main/scala/org/bdgenomics/adam/models/TrackedLayout.scala
+++ /dev/null
@@ -1,96 +0,0 @@
-/**
- * Licensed to Big Data Genomics (BDG) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The BDG licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.bdgenomics.adam.models
-
-import scala.collection.mutable
-
-/**
- * A TrackedLayout is an assignment of values of some type T (which presumably are mappable to
- * a reference genome or other linear coordinate space) to 'tracks' -- that is, to integers,
- * with the guarantee that no two values assigned to the same track will overlap.
- *
- * This is the kind of data structure which is required for non-overlapping genome visualization.
- *
- * @tparam T the type of value which is to be tracked.
- */
-trait TrackedLayout[T] {
-  def numTracks: Int
-  def trackAssignments: Map[T, Int]
-}
-
-object TrackedLayout {
-
-  def overlaps[T](rec1: T, rec2: T)(implicit rm: ReferenceMapping[T]): Boolean = {
-    val ref1 = rm.getReferenceRegion(rec1)
-    val ref2 = rm.getReferenceRegion(rec2)
-    ref1.overlaps(ref2)
-  }
-}
-
-/**
- * An implementation of TrackedLayout which takes a sequence of ReferenceMappable values,
- * and lays them out <i>in order</i> (i.e. from first-to-last) in the naive way: for each
- * value, it looks for the track with the lowest index that doesn't already have an overlapping
- * value, and it doesn't use any special data structures (it just does a linear search for each
- * track.)
- *
- * @param reads The set of values (i.e. "reads", but anything that is mappable to the reference
- *              genome ultimately) to lay out in tracks
- * @param mapping The (implicit) reference mapping which converts values to ReferenceRegions
- * @tparam T the type of value which is to be tracked.
- */
-class OrderedTrackedLayout[T](reads: Traversable[T])(implicit val mapping: ReferenceMapping[T]) extends TrackedLayout[T] {
-
-  private var trackBuilder = new mutable.ListBuffer[Track]()
-  reads.toSeq.foreach(findAndAddToTrack)
-  trackBuilder = trackBuilder.filter(_.records.nonEmpty)
-
-  val numTracks = trackBuilder.size
-  val trackAssignments: Map[T, Int] =
-    Map(trackBuilder.toList.zip(0 to numTracks).flatMap {
-      case (track: Track, idx: Int) => track.records.map(_ -> idx)
-    }: _*)
-
-  private def findAndAddToTrack(rec: T) {
-    val reg = mapping.getReferenceRegion(rec)
-    if (reg != null) {
-      val track: Option[Track] = trackBuilder.find(track => !track.conflicts(rec))
-      track.map(_ += rec).getOrElse(addTrack(new Track(rec)))
-    }
-  }
-
-  private def addTrack(t: Track): Track = {
-    trackBuilder += t
-    t
-  }
-
-  private class Track(val initial: T) {
-
-    val records = new mutable.ListBuffer[T]()
-    records += initial
-
-    def +=(rec: T): Track = {
-      records += rec
-      this
-    }
-
-    def conflicts(rec: T): Boolean =
-      records.exists(r => TrackedLayout.overlaps(r, rec))
-  }
-
-}
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/models/TrackedLayoutSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/models/TrackedLayoutSuite.scala
deleted file mode 100644
index 5c63d9e645..0000000000
--- a/adam-core/src/test/scala/org/bdgenomics/adam/models/TrackedLayoutSuite.scala
+++ /dev/null
@@ -1,88 +0,0 @@
-/**
- * Licensed to Big Data Genomics (BDG) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The BDG licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.bdgenomics.adam.models
-
-import org.bdgenomics.adam.rich.ReferenceMappingContext._
-import org.bdgenomics.formats.avro.{ AlignmentRecord, Contig }
-import org.scalatest.FunSuite
-
-class TrackedLayoutSuite extends FunSuite {
-
-  def rec(contig: String = null, start: Int = 0, cigar: String = null, end: Int = 0, readMapped: Boolean = true, firstOfPair: Boolean = true): AlignmentRecord = {
-    val c = Contig.newBuilder().setContigName(contig).build()
-
-    AlignmentRecord.newBuilder()
-      .setContig(c)
-      .setReadMapped(readMapped)
-      .setFirstOfPair(firstOfPair)
-      .setStart(start)
-      .setCigar(cigar)
-      .setEnd(end)
-      .build()
-  }
-
-  test("OrderedTrackedLayout lays out no records into zero tracks") {
-    val layout = new OrderedTrackedLayout[AlignmentRecord](Seq())
-    assert(layout.numTracks === 0)
-  }
-
-  test("OrderedTrackedLayout lays out AlignmentRecords left-to-right in the order they're passed") {
-    val (r1, r2, r3, r4) = (
-      rec("chr1", 100, "100M", 200),
-      rec("chr1", 150, "100M", 250),
-      rec("chr1", 200, "100M", 300),
-      rec("chr2", 200, "100M", 300))
-
-    val recs = Seq(r1, r2, r3, r4)
-    val layout: OrderedTrackedLayout[AlignmentRecord] = new OrderedTrackedLayout(recs)
-
-    // Just making sure... r4 shouldn't overlap r1-3
-    val rm: ReferenceMapping[AlignmentRecord] = AlignmentRecordReferenceMapping
-    val refs123 = Seq(r1, r2, r3).map(rm.getReferenceRegion)
-    assert(!refs123.exists(rm.getReferenceRegion(r4).overlaps))
-
-    // Now, test the correct track assignments of each record
-    assert(layout.trackAssignments.get(r1) === Some(0))
-    assert(layout.trackAssignments.get(r2) === Some(1))
-    assert(layout.trackAssignments.get(r3) === Some(0))
-    assert(layout.trackAssignments.get(r4) === Some(0))
-    assert(layout.numTracks === 2)
-  }
-
-  test("OrderedTrackedLayout can handle unaligned reads") {
-    val (r1, r2, r3, r4) = (
-      rec("chr1", 100, "100M", 200),
-      rec("chr1", 150, "100M", 250),
-      rec("chr1", 200, "100M", 300),
-      rec(readMapped = false))
-
-    val recs = Seq(r1, r2, r3, r4)
-    val layout: OrderedTrackedLayout[AlignmentRecord] = new OrderedTrackedLayout(recs)
-
-    // Just making sure... r4 shouldn't overlap r1-3
-    val rm: ReferenceMapping[AlignmentRecord] = AlignmentRecordReferenceMapping
-    val refs123 = Seq(r1, r2, r3).map(rm.getReferenceRegion)
-
-    // Now, test the correct track assignments of each record
-    assert(layout.trackAssignments.get(r1) === Some(0))
-    assert(layout.trackAssignments.get(r2) === Some(1))
-    assert(layout.trackAssignments.get(r3) === Some(0))
-    assert(layout.trackAssignments.get(r4) === None)
-    assert(layout.numTracks === 2)
-  }
-}