Rename the Variation record to Variant; add a precomputed SNV characteristics search

Model/bin/jbrowseTracks

@@ -89,6 +89,10 @@ else {
         );
   }
   elsif($tracks eq 'syntenyTracks' || $tracks eq 'geneticVariationTracks') {
+    # geneticVariationTracks deliberately does NOT include the dnaseq endpoint. The merged
+    # short-variant VCF is served by organismSpecific, so this set already has it, and
+    # staying out of dnaseq keeps the gene page's SNP link at ~100 track configs instead of
+    # ~1600 per-sample coverage and density ones.
     @include = ("/a/jbrowse/tracks/${organismAbbrev}/tracks.conf",
                 "/a/service/jbrowse/organismSpecific/${organismAbbrev}",
                 "/a/jbrowse/jbrowse_embed.conf"
@@ -118,7 +122,7 @@ else {
   }
   else {
   @include = ("/a/jbrowse/tracks/${organismAbbrev}/tracks.conf",
-#              "/a/service/jbrowse/dnaseq/${organismAbbrev}",
+              "/a/service/jbrowse/dnaseq/${organismAbbrev}",
               "/a/service/jbrowse/rnaseq/${organismAbbrev}",
               "/a/service/jbrowse/chipseq/${organismAbbrev}",
               "/a/service/jbrowse/rnaseqJunctions/${organismAbbrev}",

Model/lib/dst/jbrowse.dst

@@ -98,28 +98,23 @@ prop=datasetName
 prop=datasetDisplayName
 prop=shortAttribution
 prop=summary
-prop=hasCNVData
 >templateTextStart<
 dnaseq::${datasetName}::datasetName=${datasetName}
 dnaseq::${datasetName}::datasetDisplayName=${datasetDisplayName}
 dnaseq::${datasetName}::shortAttribution=${shortAttribution}
 dnaseq::${datasetName}::summary=${summary}
-dnaseq::${datasetName}::hasCNVData=${hasCNVData}
 dnaseq::${datasetName}::category=Genetic Variation
 dnaseq::${datasetName}::yScalePosition=left
 dnaseq::${datasetName}::chunkSizeLimit=50000000
 dnaseq::${datasetName}::subCategory=DNA-Seq
 >templateTextEnd<
 
-[templateStart]
-name=jbrowseDnaSeqSampleBuildProps
-anchorFile=ApiCommonModel/Model/lib/jbrowse/auto_generated/${organismAbbrev}/datasetAndPresenterProps.conf
-prop=organismAbbrev
-prop=datasetName
-prop=sampleName
->templateTextStart<
-dnaseq::${datasetName}::sampleNames::${sampleName}=${sampleName}
->templateTextEnd<
+# NOTE: there is deliberately no per-sample dnaseq template. The sample list, and which
+# measures each sample has, are read from the webservices tree at request time by
+# JbrowseDnaSeqTracks.pm - the pipeline that writes those files is the only thing that
+# knows them, and LOH in particular exists only for diploid organisms. hasCNVData is
+# likewise not emitted: presenters still declare it but _normalisedCoverage.bw is now
+# written regardless, so the flag no longer describes the data.
 
 [templateStart]
 name=jbrowseChipChipExperSampleBuildProps

Model/lib/jbrowse/datasetAndPresenterProps.conf

@@ -8,7 +8,9 @@
 
 # TEMPLATE_ANCHOR jbrowseDnaSeqBuildProps
 
-# TEMPLATE_ANCHOR jbrowseDnaSeqSampleBuildProps
+# NOTE: there is deliberately no jbrowseDnaSeqSampleBuildProps anchor. Per-sample dnaseq
+# properties are not injected; JbrowseDnaSeqTracks.pm reads the sample list, and which
+# measures each sample has, from the webservices tree at request time.
 
 # TEMPLATE_ANCHOR jbrowseChipChipExperSampleBuildProps
 

Model/lib/jbrowse/functions.conf

@@ -2274,3 +2274,71 @@ auxiliaryUtrColor = function( feature, variableName, glyphObject, track ) {
   return strand == 1 ? "dodgerblue" : "tomato";
  }
 
+
+# --- Short variant tracks (the dnaseq pipeline's merged annotated VCF) ----------------
+# Both the shape and the colour of a variant are resolved PER FEATURE by JBrowse
+# (CanvasFeatures getGlyph/getStyle both go through getConfForFeature), so a single track
+# can mix glyphs and colours rather than needing one track per variant class.
+
+# Both are deliberately self-contained rather than delegating through
+# track.browser.config the way snpColorFxn does. getConfForFeature does not always supply
+# the track argument - resolving glyph through it passes a null track - and neither
+# function needs anything but the feature, so a track deref would only add a way to throw.
+#
+# JBrowse's VCF parser types variants for us; the values it emits are exactly 'SNV',
+# 'insertion' and 'deletion'. Substitutions get a diamond, indels a box - a box also
+# reads better for an indel because it renders at the variant's real width, whereas an
+# SNV is always one base.
+variantGlyphFxn = function( feature, variableName, glyphObject, track ) {
+   return feature.get("type") === "SNV"
+     ? "EbrcTracks/View/FeatureGlyph/Diamond"
+     : "JBrowse/View/FeatureGlyph/Box";
+ }
+
+# Colour by EFFECT CLASS, following the varianteffect plugin's convention: green
+# synonymous, purple non-synonymous, red truncating, blue intron/other. Read from
+# snpEff's Annotation (field 2 of each pipe-delimited ANN entry), not Annotation_Impact
+# (field 3) - impact only has four ordinal levels and rendered as a warm ramp its top two
+# were indistinguishable at glyph size.
+#
+# The exact hexes matter. The plugin's nominal green/red pair sits at deltaE 3.3 under
+# deuteranopia - a hard fail, on the single most consequential pair here (a silent change
+# vs a truncation). Under deuteranopia red and green separate mainly by LIGHTNESS, so red
+# is deliberately dark (#b71c1c): that lifts the worst all-pairs separation to deltaE 9.7
+# with every colour clearing 3:1 on white. Do not "brighten" the red without re-running
+# the check.
+#
+# A variant may carry several ANN entries, one per affected transcript, and snpEff joins
+# compound effects on '&' - so scan every entry for the most severe class rather than
+# trusting the first. Tests run most-severe-first, which is what makes the compound case
+# (missense_variant&splice_region_variant -> non-synonymous) fall out correctly.
+#
+# NOTE: no blank lines inside the function body. A blank line terminates a multi-line
+# value in this file's parser, so the value would be truncated mid-function, fail to
+# compile, and be left as a plain string - silently, with the track then rendering in a
+# default colour. No existing function here contains one either.
+variantEffectColorFxn = function( feature, variableName, glyphObject, track ) {
+   var truncatingColor = '#b71c1c';
+   var nonSynonymousColor = '#7b3294';
+   var synonymousColor = '#43a047';
+   var otherColor = '#2c7bb6';
+   var ann = feature.get("ANN");
+   var entries = ann && ann.values ? ann.values : null;
+   if (!entries || !entries.length) {
+      return otherColor;
+   }
+   var effects = '';
+   for (var i = 0; i < entries.length; i++) {
+      effects = effects + '&' + String(entries[i]).split("|")[1];
+   }
+   if (/stop_gained|stop_lost|start_lost|frameshift|splice_acceptor|splice_donor|exon_loss|transcript_ablation/.test(effects)) {
+      return truncatingColor;
+   }
+   if (/missense|inframe_insertion|inframe_deletion|protein_altering|rare_amino_acid|initiator_codon/.test(effects)) {
+      return nonSynonymousColor;
+   }
+   if (/synonymous_variant|stop_retained|start_retained/.test(effects)) {
+      return synonymousColor;
+   }
+   return otherColor;
+ }

Model/lib/perl/JBrowseTrackConfig/MultiBigWigTrackConfig.pm

@@ -31,13 +31,21 @@ sub new {
 
     my $alignmentDisplay;
 
+    # has_alignment => 0 is for callers with no read-alignment split at all (dnaseq).
+    # Without it every track claims "unique and non-unique", which then shows up as an
+    # RNA-Seq Alignment facet value on a track that has no such notion.
+    my $hasAlignment = exists($args->{has_alignment}) ? $args->{has_alignment} : 1;
+
     if($alignment && $alignment eq 'unique') {
       $alignmentDisplay = "Unique Only";
-    } 
-    else {
+    }
+    elsif($hasAlignment) {
       $alignmentDisplay = "Unique And Non-Unique";
       $self->setAlignment("unique and non-unique");
     }
+    else {
+      $alignmentDisplay = "";
+    }
 
     my $subclassName = ref($self);
     if($subclassName =~ /Density/) {
@@ -63,6 +71,17 @@ sub new {
 
     }
 
+    # Explicit label/id/track type win, and are applied last so they also beat the
+    # jbrowse2 branch above. Every derived form is keyed on the DATASET, which is fine
+    # for one multi track per dataset but collides immediately for a caller emitting one
+    # per sample - label is the JBrowse track id and must be unique across the response.
+    #
+    # NOTE track_type_display is deliberately NOT overridable here: the ::Density and ::XY
+    # subclasses set it after SUPER::new returns, so anything set here would be silently
+    # clobbered. A caller wanting its own wording calls setTrackTypeDisplay on the
+    # constructed object instead.
+    $self->setLabel($args->{label}) if(defined($args->{label}) && length($args->{label}));
+    $self->setId($args->{id}) if(defined($args->{id}) && length($args->{id}));
 
     return $self;
 }

Model/lib/perl/JBrowseTrackConfig/SingleCoverageTrackConfig.pm

@@ -45,14 +45,30 @@ sub new {
     $self->setId("$studyDisplayName - $displayName $displayNameSuffix");
     }
 
-    if ($dbid){
-    $self->setLabel("$datasetName $dbid Coverage");        
+    # An explicit label wins. label is the JBrowse track id, so it must be unique across
+    # the whole response; callers that emit several tracks per sample (dnaseq emits up to
+    # five measures each) need that uniqueness by construction rather than by luck of the
+    # sample names happening to be distinct. Both derived forms below remain the default,
+    # so existing callers are unaffected.
+    if (defined($args->{label}) && length($args->{label})) {
+    $self->setLabel($args->{label});
+    }
+    elsif ($dbid){
+    $self->setLabel("$datasetName $dbid Coverage");
     }
     else {
     $self->setLabel("$displayName $displayNameSuffix");
     }
 
-    if (!defined($order) && !defined($dbid)) {
+    # An explicit track type display wins; this string is shown to users in the track
+    # selector. The ploidy-normalised default below is only correct for the CNV coverage
+    # track, which was the sole order-less and dbid-less caller when it was written; a
+    # caller emitting other per-sample measures (SNP density, LOH, ...) must be able to
+    # say what its track actually is instead of inheriting that label.
+    if (defined($args->{track_type_display}) && length($args->{track_type_display})) {
+    $self->setTrackTypeDisplay($args->{track_type_display});
+    }
+    elsif (!defined($order) && !defined($dbid)) {
     $self->setTrackTypeDisplay("Coverage (ploidy Normalized)");;
     }
 

Model/lib/perl/JBrowseTrackConfig/VCFStore.pm

@@ -11,17 +11,16 @@ sub setUrlTemplate {
 }
 
 
-sub getChunkSizeLimit  {$_[0]->{chunk_size_limit} }
-sub setChunkSizeLimit {$_[0]->{chunk_size_limit} = $_[1]}
-
 sub new {
     my ($class, $args) = @_;
     my $self = $class->SUPER::new($args);
 
     #$self->setUrlTemplate($args->{url_template});
     #$self->setType("JBrowse/View/Track/CanvasVariants");
 
-    $self->setChunkSizeLimit(10000000);
+    # NOTE: chunkSizeLimit is not set here. It is emitted by VcfTrackConfig, which is what
+    # actually reaches the track config; this class used to set a chunk_size_limit that
+    # nothing ever read, so raising it here looked effective and did nothing.
 
     if($self->getApplicationType() eq 'jbrowse' || $self->getApplicationType() eq 'apollo') {
         $self->setStoreType("JBrowse/Store/SeqFeature/VCFTabix");

Model/lib/perl/JBrowseTrackConfig/VcfTrackConfig.pm

@@ -38,8 +38,19 @@ sub new {
     }
 
     $self->setStore($store);
-    $self->setGlyph("EbrcTracks/View/FeatureGlyph/Diamond");
-    $self->setTrackTypeDisplay("VCF from VectorBase");
+
+    # A caller may supply its own glyph, including a "{someFxn}" reference resolved per
+    # feature, so one track can shape SNVs and indels differently. Defaults to the diamond
+    # every existing caller expects.
+    $self->setGlyph($args->{glyph} ? $args->{glyph} : "EbrcTracks/View/FeatureGlyph/Diamond");
+
+    # The historic default names VectorBase because the only caller was VectorBase's
+    # per-sample ebi_VCF tracks. It is shown to users in the track selector, so a caller
+    # serving some other VCF must be able to say what it actually is rather than
+    # mislabel it.
+    $self->setTrackTypeDisplay($args->{track_type_display}
+                                 ? $args->{track_type_display}
+                                 : "VCF from VectorBase");
 
     return $self;
 }
@@ -50,7 +61,23 @@ sub getJBrowseObject{
     my $jbrowseObject = $self->SUPER::getJBrowseObject();
 
     $jbrowseObject->{urlTemplate}= $self->getStore()->getUrlTemplate();
-    $jbrowseObject->{chunkSizeLimit} = '10000000';
+
+    # Store-level fetch ceilings, not allocations: when a region needs more than this the
+    # store abandons it rather than rendering. The merged multi-sample call sets are far
+    # larger than the per-sample VCFs these were first sized for. Emitted as numbers
+    # rather than the quoted string this used to send.
+    $jbrowseObject->{chunkSizeLimit} = 50000000;
+    $jbrowseObject->{fetchSizeLimit} = 150000000;
+
+    # This - NOT chunkSizeLimit - is what produces "Too many features to show" when zoomed
+    # out. CanvasFeatures.fillBlock refuses to draw a block whose feature density exceeds
+    # it, and the JBrowse default is 0.5 features/pixel. The merged call set runs about 6.8
+    # variants/kb, so in a ~1000px window a 300kb view is already ~2 features/pixel and a
+    # full 3.3Mb P. falciparum chromosome is ~22 - both far past 0.5. 50 clears a whole
+    # chromosome with roughly 2x headroom. Deliberately not the 9999999 that
+    # RNASeqJunctionTrackConfig uses: that invites drawing 100k+ glyphs at genome scale.
+    $jbrowseObject->{maxFeatureScreenDensity} = 50;
+
     $jbrowseObject->{glyph} = $self->getGlyph();
     return $jbrowseObject;
 }