Merge pull request #542 from erictu/basic-viz

Variants Visualization

adam-cli/src/main/scala/org/bdgenomics/adam/cli/VizReads.scala

@@ -19,14 +19,16 @@ 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.rdd.read.AlignmentRecordContext._
-import org.bdgenomics.adam.rich.ReferenceMappingContext.AlignmentRecordReferenceMapping
-import org.bdgenomics.formats.avro.AlignmentRecord
+import org.bdgenomics.adam.rdd.variation.VariationContext._
+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 }
@@ -40,8 +42,9 @@ object VizReads extends ADAMCommandCompanion {
  var refName = ""
  var inputPath = ""
  var reads: RDD[AlignmentRecord] = null
+ var variants: RDD[Genotype] = null
 
- val trackHeight = 5
+ val trackHeight = 10
  val width = 1200
  val height = 400
  val base = 50
@@ -61,6 +64,19 @@ object VizReads extends ADAMCommandCompanion {
  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]
@@ -96,6 +112,7 @@ object VizReads extends ADAMCommandCompanion {
 }
 
 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 {
@@ -111,7 +128,7 @@ class VizReadsArgs extends Args4jBase with ParquetArgs {
 
 class VizServlet extends ScalatraServlet with JacksonJsonSupport {
  protected implicit val jsonFormats: Formats = DefaultFormats
- var regInfo = ReferenceRegion(VizReads.refName, 0, 100)
+ var regInfo = ReferenceRegion(VizReads.refName, 0, 200)
  var filteredLayout: OrderedTrackedLayout[AlignmentRecord] = null
  var filteredArray: Array[AlignmentRecord] = null
 
@@ -159,6 +176,30 @@ class VizServlet extends ScalatraServlet with JacksonJsonSupport {
  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] {
@@ -168,7 +209,14 @@ class VizReads(protected val args: VizReadsArgs) extends ADAMSparkCommand[VizRea
  VizReads.refName = args.refName
 
  val proj = Projection(contig, readMapped, readName, start, end)
- VizReads.reads = sc.loadAlignments(args.inputPath, projection = Some(proj))
+
+ 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()
@@ -178,7 +226,7 @@ class VizReads(protected val args: VizReadsArgs) extends ADAMSparkCommand[VizRea
  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()
  }
-
 }

adam-cli/src/main/webapp/WEB-INF/layouts/reads.ssp

@@ -26,13 +26,13 @@
  .highlight {
  font-weight:700;
  }
-  h2 {
-  text-align: center;
-  margin: 0 0 10px 0;
-  color: #999999;
-  font-weight:300;
-  }
-  ul {
+  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;