thread viewAsPairs through to Pileup{Track,Cache}

src/main/PileupCache.js

@@ -36,30 +36,36 @@ export type VisualGroup = {
   alignments: VisualAlignment[];
 };
 
-// read name would make a good key, but paired reads from different contigs
-// shouldn't be grouped visually. Hence we use read name + contig.
-function groupKey(read: Alignment): string {
-  return `${read.name}:${read.ref}`;
-}
-
 // This class provides data management for the visualization, grouping paired
 // reads and managing the pileup.
 class PileupCache {
   // maps groupKey to VisualGroup
   groups: {[key: string]: VisualGroup};
   refToPileup: {[key: string]: Array<Interval[]>};
   referenceSource: TwoBitSource;
+  viewAsPairs: boolean;
 
-  constructor(referenceSource: TwoBitSource) {
+  constructor(referenceSource: TwoBitSource, viewAsPairs: boolean) {
     this.groups = {};
     this.refToPileup = {};
     this.referenceSource = referenceSource;
+    this.viewAsPairs = viewAsPairs;
+  }
+
+  // read name would make a good key, but paired reads from different contigs
+  // shouldn't be grouped visually. Hence we use read name + contig.
+  groupKey(read: Alignment): string {
+    if (this.viewAsPairs) {
+      return `${read.name}:${read.ref}`;
+    } else {
+      return read.getKey();
+    }
   }
 
   // Load a new read into the visualization cache.
   // Calling this multiple times with the same read is a no-op.
   addAlignment(read: Alignment) {
-    var key = groupKey(read),
+    var key = this.groupKey(read),
         range = read.getInterval();
 
     if (!(key in this.groups)) {
@@ -91,13 +97,17 @@ class PileupCache {
     if (group.alignments.length == 1) {
       // This is the first read in the group. Infer its span from its mate properties.
       // TODO: if the mate Alignment is also available, it would be better to use that.
-      var intervals = [range];
-      var mateProps = read.getMateProperties();
-      if (mateProps && mateProps.ref && mateProps.ref == read.ref) {
-        mateInterval = new ContigInterval(mateProps.ref, mateProps.pos, mateProps.pos + range.length());
-        intervals.push(mateInterval);
+      if (this.viewAsPairs) {
+        var mateProps = read.getMateProperties();
+        var intervals = [range];
+        if (mateProps && mateProps.ref && mateProps.ref == read.ref) {
+          mateInterval = new ContigInterval(mateProps.ref, mateProps.pos, mateProps.pos + range.length());
+          intervals.push(mateInterval);
+        }
+        group = _.extend(group, spanAndInsert(intervals));
+      } else {
+        group.span = range;
       }
-      group = _.extend(group, spanAndInsert(intervals));
 
       if (!(read.ref in this.refToPileup)) {
         this.refToPileup[read.ref] = [];
@@ -160,7 +170,7 @@ function spanAndInsert(intervals: ContigInterval<string>[]) {
   if (intervals.length == 1) {
     return {insert: null, span: intervals[0]};
   } else if (intervals.length !=2) {
-    throw `Called spanAndInsert with ${intervals.length} \in [1, 2]`;
+    throw `Called spanAndInsert with ${intervals.length} \notin [1, 2]`;
   }
 
   if (!intervals[0].chrOnContig(intervals[1].contig)) {

src/main/PileupTrack.js

@@ -231,7 +231,7 @@ class PileupTrack extends React.Component {
   }
 
   componentDidMount() {
-    this.cache = new PileupCache(this.props.referenceSource);
+    this.cache = new PileupCache(this.props.referenceSource, this.props.options.viewAsPairs);
     this.props.source.on('newdata', range => {
       this.updateReads(range);
       this.updateVisualization();
@@ -363,6 +363,7 @@ PileupTrack.propTypes = {
   range: types.GenomeRange.isRequired,
   source: React.PropTypes.object.isRequired,
   referenceSource: React.PropTypes.object.isRequired,
+  options: React.PropTypes.object
 };
 PileupTrack.displayName = 'pileup';
 

src/main/pileup.js

@@ -108,8 +108,11 @@ function create(elOrId: string|Element, params: PileupParams): Pileup {
 
 type VizObject = ((options: ?Object) => {component: React.Component, options:?Object});
 
-function makeVizObject(component: React.Component): VizObject {
-  return options => ({component, options});
+function makeVizObject(component: React.Component, defaultOptions: ?Object): VizObject {
+  return options => {
+    options = _.extend({}, defaultOptions, options);
+    return {component, options};
+  };
 }
 
 var pileup = {
@@ -129,7 +132,7 @@ var pileup = {
     location: makeVizObject(LocationTrack),
     scale:    makeVizObject(ScaleTrack),
     variants: makeVizObject(VariantTrack),
-    pileup:   makeVizObject(PileupTrack)
+    pileup:   makeVizObject(PileupTrack, {viewAsPairs: false})
   }
 };
 

src/test/PileupCache-test.js

@@ -73,15 +73,15 @@ describe('PileupCache', function() {
     return new ContigInterval(chr, start, end);
   }
 
-  function makeCache(args) {
-    var cache = new PileupCache(fakeSource);
+  function makeCache(args, viewAsPairs: boolean) {
+    var cache = new PileupCache(fakeSource, viewAsPairs);
     _.flatten(args).forEach(read => cache.addAlignment(read));
     return cache;
   }
 
   it('should group read pairs', function() {
     var cache = makeCache(makeReadPair(ci('chr1', 100, 200),
-                                       ci('chr1', 300, 400)));
+                                       ci('chr1', 300, 400)), true /* viewAsPairs */);
 
     var groups = _.values(cache.groups);
     expect(groups).to.have.length(1);
@@ -104,7 +104,7 @@ describe('PileupCache', function() {
       makeReadPair(ci('chr1', 100, 200), ci('chr1', 300, 400)),  // A
       makeReadPair(ci('chr1', 300, 400), ci('chr1', 500, 600)),  // B
       makeReadPair(ci('chr1', 700, 800), ci('chr1', 500, 600))   // C
-    ]);
+    ], true /* viewAsPairs */);
 
     var groups = _.values(cache.groups);
     expect(groups).to.have.length(3);
@@ -119,7 +119,7 @@ describe('PileupCache', function() {
     var cache = makeCache([
       makeReadPair(ci('chr1', 100, 200), ci('chr1', 800, 900)),
       makeReadPair(ci('chr1', 300, 400), ci('chr1', 500, 600))
-    ]);
+    ], true /* viewAsPairs */);
 
     var groups = _.values(cache.groups);
     expect(groups).to.have.length(2);
@@ -128,9 +128,21 @@ describe('PileupCache', function() {
     expect(cache.pileupHeightForRef('chr1')).to.equal(2);
   });
 
+  it('should pack unpaired reads more tightly', function() {
+    // Same as the previous test, but with viewAsPairs = false.
+    // When the inserts aren't rendered, the reads all fit on a single line.
+    var cache = makeCache([
+      makeReadPair(ci('chr1', 100, 200), ci('chr1', 800, 900)),
+      makeReadPair(ci('chr1', 300, 400), ci('chr1', 500, 600))
+    ], false /* viewAsPairs */);
+    var groups = _.values(cache.groups);
+    expect(groups).to.have.length(4);
+    expect(cache.pileupHeightForRef('chr1')).to.equal(1);
+  });
+
   it('should separate pairs on differing contigs', function() {
     var cache = makeCache(makeReadPair(ci('chr1', 100, 200),
-                                       ci('chr2', 150, 250)));
+                                       ci('chr2', 150, 250)), true /* viewAsPairs */);
 
     var groups = _.values(cache.groups);
     expect(groups).to.have.length(2);
@@ -151,7 +163,7 @@ describe('PileupCache', function() {
       makeReadPair(ci('chr1', 100, 200), ci('chr1', 800, 900)),
       makeReadPair(ci('chr1', 300, 400), ci('chr1', 500, 600)),
       makeReadPair(ci('chr2', 100, 200), ci('chr2', 300, 400))
-    ]);
+    ], true /* viewAsPairs */);
 
     expect(cache.getGroupsOverlapping(ci('chr1', 50, 150))).to.have.length(1);
     expect(cache.getGroupsOverlapping(ci('chr1', 50, 350))).to.have.length(2);