744c3f21361148e959397572e346516a81ea52ed
braney
Mon Aug 31 13:21:01 2026 -0700
Replace the dead snp track type with bed in thirteen trackDb settings
Thirteen settings in the library declared the type snp and nothing else. There
is no such track any more. hg38 and hg19 both have zero tracks of that type,
and nothing in the track engine dispatches on it: the only startsWith("snp",
...) left, at cgilib/snp125.c:318, tests the track name rather than the type.
The dbSNP tracks are bigDbSnp and "bed 6 +". So snp is not a missing type here,
it is a type that went away and took thirteen type lists with it.
Every one of them is used on bed today, between 2 and 4047 tracks each, and
each has a reader that a bed track reaches: snp125Ui.c for the ortho tables,
hapmapTrack.c for hapmapPhase, variation.c for defaultMaxWeight, and hgc.c for
the rest.
defaultGeneTracks gets bed and bigDbSnp. Its 16 bigDbSnp tracks are real, not
convention: snp153OfferGeneTracksForFunction reads the setting at hui.c:4923
and bigDbSnpCfgUi calls that function at hui.c:4999. None of the other twelve
is read on a bigDbSnp path.
Two of the thirteen were missing from the earlier survey of this family.
chimpMacaqueOrthoTable is a separate setting from chimpOrangMacOrthoTable and
is read at snp125Ui.c:16. codingAnnoLabel_<table> looked unused because hgc.c
builds the setting name at run time, at hgc.c:20153 inside
printSnpAlleleAndOrthos.
The two remaining snp spans are left alone on purpose. Neither is a setting:
one documents the snp track type itself and already says "type bed 6 +", and
the other is the example track stanza beneath it.
None of these thirteen has a row in the hub spec, which is correct, since they
all name a SQL table or a SQL-backed gene track. So the generated
trackDbSettings.yaml and .json do not change.
refs #37908
diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
index 2d0614344d4..ad1f694d7e6 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
@@ -4706,129 +4706,129 @@
followed by the 3-digit dbSNP build number </code></div>
<P>UCSC's subset of dbSNP could be described as "bed 6 + 19"
and is produced by a complex process starting with downloading
several database dump files and fasta files from dbSNP, and ending
with the creation of snp<em>NNN</em> and several auxiliary data
tables. This type is not supported as a custom track type.</P>
</DIV>
<DIV class="chimpDb"><span class = "types snp"></span>
<div class="format"><code>chimpDb <db></code></div>
<P>If chimp chains/nets were used to identify the chimp reference
assembly allele at the location homologous to the human SNP, this
specifies which chimp genome assembly was used, e.g. <code>panTro2</code>.</P>
</DIV>
-<DIV class="chimpMacaqueOrthoTable"><span class="types snp"></span>
+<DIV class="chimpMacaqueOrthoTable"><span class="types bed"></span>
<div class="format"><code>chimpMacaqueOrthoTable <table></code></div>
<P>If chains/nets from chimp and rhesus macaque were use to identify
the chimp or macaque reference assembly allele at the location
homologous to the human SNP, this specifies the database table
that contains the mapped alleles.</P>
</DIV>
-<DIV class="chimpOrangMacOrthoTable"><span class="types snp"></span>
+<DIV class="chimpOrangMacOrthoTable"><span class="types bed"></span>
<div class="format"><code>chimpOrangMacOrthoTable <table></code></div>
<P>If chains/nets from chimp, orangutan and rhesus macaque were use to identify
the chimp/orangutan/macaque reference assembly allele at the location
homologous to the human SNP, this specifies the database table
that contains the mapped alleles.</P>
</DIV>
-<DIV class="codingAnnoLabel_table"><span class="types snp"></span>
+<DIV class="codingAnnoLabel_table"><span class="types bed"></span>
<div class="format"><code>codingAnnoLabel_<table> <text></code></div>
<P><I>Deprecated; will probably be removed.</I>
This specifies a text label for display of <table>'s
predictions of a SNP's effect on a protein-coding gene.</P>
</DIV>
-<DIV class="codingAnnotations"><span class="types snp"></span>
+<DIV class="codingAnnotations"><span class="types bed"></span>
<div class="format"><code>codingAnnotations <table>[,table]</code></div>
<P><I>Deprecated; will probably be removed.</I>
This specifies one or more tables containing predictions of SNP
effects on protein-coding genes.</P>
</DIV>
-<DIV class="defaultGeneTracks"><span class="types snp"></span>
+<DIV class="defaultGeneTracks"><span class="types bed bigDbSnp"></span>
<div class="format"><code>defaultGeneTracks <genesTrack>[,genesTrack]</code></div>
<P>The details page of a SNP can display the predicted functional
affect on a gene from any genePred track.
Since there are often many gene tracks and models, the prediction
will depend upon the gene model used. The user has a chance to
choose from those available, but this setting establishes
a default gene track or tracks to base predictions on.</P>
<P><B>Example</B>:</P>
<pre> defaultGeneTracks knownGenes</pre>
</DIV>
-<DIV class="defaultMaxWeight"><span class="types snp"></span>
+<DIV class="defaultMaxWeight"><span class="types bed"></span>
<div class="format"><code>defaultMaxWeight <1|2|3></code></div>
<P>dbSNP assigns a weight of 1, 2 or 3 to each variant, depending
on how many distinct mappings a variant's flanking sequences have
to the genome.
If this is set to <code>1</code>, only uniquely mapped variants will
be displayed by default. If <code>2</code>, only uniquely mapped
variants and variants with a small number of duplicate mappings will
be displayed. If <code>3</code>, all variants will be shown regardless
of weight. Note: some tables such as snp<em>NNN</em>Common and
snp<em>NNN</em>Flagged contain only uniquely mapped variants, so this
setting has no effect on those tables.</P>
</DIV>
-<DIV class="hapmapPhase"><span class="types snp"></span>
+<DIV class="hapmapPhase"><span class="types bed"></span>
<div class="format"><code>hapmapPhase <II|III></code></div>
<P>The SNP details page looks for the SNP's ID in HapMap track tables
that have different names and contents depending on whether they
were loaded from HapMap phase II or HapMap phase III data.
(This setting is also used by HapMap SNPs tracks.)</P>
</DIV>
-<DIV class="macaqueDb"><span class="types snp"></span>
+<DIV class="macaqueDb"><span class="types bed"></span>
<div class="format"><code>macaqueDb <db></code></div>
<P>If macaque chains/nets were used to identify the macaque reference
assembly allele at the location homologous to the human SNP, this
specifies which macaque genome assembly was used, e.g. <code>rheMac2</code>.</P>
</DIV>
-<DIV class="orangDb"><span class="types snp"></span>
+<DIV class="orangDb"><span class="types bed"></span>
<div class="format"><code>orangDb <db></code></div>
<P>If orangutan chains/nets were used to identify the orangutan reference
assembly allele at the location homologous to the human SNP, this
specifies which orangutan genome assembly was used, e.g. <code>ponAbe2</code>.</P>
</DIV>
-<DIV class="snpExceptions"><span class="types snp"></span>
+<DIV class="snpExceptions"><span class="types bed"></span>
<div class="format"><code>snpExceptions <table></code></div>
<P>This specifies an auxiliary table that contains annotations of unusual
properties of variants. This setting applies only to versions prior to dbSNP
build 132; starting with build 132, exceptions are incorporated into the
main snp<em>NNN</em> table and an auxiliary table is no longer needed.</P>
</DIV>
-<DIV class="snpExceptionDesc"><span class="types snp"></span>
+<DIV class="snpExceptionDesc"><span class="types bed"></span>
<div class="format"><code>snpExceptionDesc <table></code></div>
<P>This specifies an auxiliary table that maps exception keywords
to one-sentence descriptions.</P>
</DIV>
-<DIV class="snpSeq"><span class="types snp"></span>
+<DIV class="snpSeq"><span class="types bed"></span>
<div class="format"><code>snpSeq <table></code></div>
<P>This specifies an auxiliary table that maps variant IDs to
file offsets at which flanking sequences are stored.</P>
</DIV>
-<DIV class="snpSeqFile"><span class="types snp"></span>
+<DIV class="snpSeqFile"><span class="types bed"></span>
<div class="format"><code>snpSeqFile <path></code></div>
<P>This specifies an auxiliary file that contains the flanking
sequences of each variant's representative submitted SNP.</P>
</DIV>
<DIV class="snp_example"><span class="types snp"></span>
<div class="format"><B>Example of a SNP track</B></div>
<pre>
track snp135Common
shortLabel Common SNPs(135)
longLabel Simple Nucleotide Polymorphisms (dbSNP 135) Found in >= 1% of Samples
group varRep
priority 99.0911
visibility dense
url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$