5aa96722c0548d51c76a430c576d1e7823c30ef7
chmalee
  Wed Aug 25 11:32:44 2021 -0700
Get double sided gaps supported in building of LRG track, refs #24672

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index a0768c0..745729f 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -98,30 +98,31 @@
 shortLabel LRG Regions
 longLabel Locus Reference Genomic (LRG) Sequences Mapped to $date Assembly
 group map
 visibility hide
 type bigBed 12 +
 noScoreFilter .
 urlLabel Link to LRG report: 
 url http://ftp.ebi.ac.uk/pub/databases/lrgex/$$.xml
 urls hgncId="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$$" ncbiAcc="https://www.ncbi.nlm.nih.gov/nuccore/$$"
 baseColorDefault diffBases
 baseColorUseSequence lrg
 indelDoubleInsert on
 indelQueryInsert on
 showDiffBasesAllScales .
 color 72,167,38
+searchIndex name
 
 track gad
 shortLabel GAD View
 longLabel Genetic Association Studies of Complex Diseases and Disorders
 group phenDis
 visibility hide
 color 200,0,0
 type bed 4
 url http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=gene=
 
 track decipher
 shortLabel Decipher CNVs
 longLabel Decipher CNVs
 group phenDis
 visibility hide
@@ -3141,30 +3142,31 @@
 urls ncbiTranscript=https://www.ncbi.nlm.nih.gov/nuccore/$$ ensemblTranscript=http://www.ensembl.org/Multi/Search/Results?site=ensembl_all;q=$$ ncbiProtein=https://www.ncbi.nlm.nih.gov/protein/$$ ensemblProtein=http://www.ensembl.org/Multi/Search/Results?site=ensembl_all;q=$$
 altColor 127,127,127
 baseColorDefault genomicCodons
 baseColorUseSequence lfExtra
 indelDoubleInsert on
 indelPolyA on
 indelQueryInsert on
 showDiffBasesAllScales .
 showDiffBasesMaxZoom 10000.0
 showCdsAllScales .
 showCdsMaxZoom 10000.0
 color 54,125,29
 urlLabel Link to LRG transcript
 url http://ftp.ebi.ac.uk/pub/databases/lrgex/$<_lrgParent>.xml#transcripts_anchor
 bigDataUrl /gbdb/$D/bbi/lrgBigPsl.bb
+searchIndex name
 release alpha
 
 track lrgTranscriptAli
 shortLabel LRG Transcripts
 longLabel Locus Reference Genomic (LRG) Fixed Transcript Annotations
 group genes
 visibility hide
 type psl .
 cdsTable lrgCds
 cdnaTable lrgCdna
 pepTable lrgPep
 baseColorDefault diffCodons
 baseColorUseCds table lrgCds
 baseColorUseSequence table lrgCdna
 indelDoubleInsert on
@@ -4022,30 +4024,38 @@
 searchType bed
 termRegex Hs\.[0-9]+
 searchPriority 20
 
 searchTable uniGene_3
 searchType psl
 termRegex Hs\.[0-9]+
 searchPriority 20
 
 searchTable HInvGeneMrna
 searchMethod exact
 searchType psl
 termRegex HIT[0-9]{9,9}
 searchPriority 50
 
+searchTable lrg
+searchMethod exact
+searchType bigBed
+termRegex LRG_[0-9]+
+semiShortCircuit 1
+searchPriority 49
+release alpha
+
 searchTable lrgBigPsl
 searchMethod exact
 searchType bigBed
 termRegex LRG_[0-9]+t[0-9]+
 semiShortCircuit 1
 searchPriority 50
 release alpha
 
 searchTable lrgTranscriptAli
 searchMethod exact
 searchType psl
 termRegex LRG_[0-9]+t[0-9]+
 semiShortCircuit 1
 searchPriority 50
 release beta,public