c7aab3a42e921c2d7019321969409bf0353abe3e
lrnassar
  Fri Mar 28 16:44:45 2025 -0700
Making MANE a default hg38 track due to popular use, and nesting the two patch sequence tracks into one composite so we can use the hideEmptySubtracks setting. The tracks are rarely used and this allows us to open up virtual real estate while still displaying them in important regions where they are vauable. Refs #35326

diff --git src/hg/makeDb/trackDb/trackDb.ra src/hg/makeDb/trackDb/trackDb.ra
index 98cfaf31ead..61a8b2e23ee 100644
--- src/hg/makeDb/trackDb/trackDb.ra
+++ src/hg/makeDb/trackDb/trackDb.ra
@@ -2,30 +2,33 @@
 
 include trackDb.chainNet.ra
 
 include trackDb.chainNet.primates.ra
 include trackDb.chainNet.euarchontoglires.ra
 include trackDb.chainNet.laurasiatheria.ra
 include trackDb.chainNet.afrotheria.ra
 include trackDb.chainNet.mammal.ra
 include trackDb.chainNet.birds.ra
 include trackDb.chainNet.sarcopterygii.ra
 include trackDb.chainNet.fish.ra
 include trackDb.chainNet.insects.ra
 include trackDb.chainNet.other.ra
 include trackDb.chainNet.asmHub.ra
 
+include patchTracks.ra beta,public
+include patchTracks.new.ra alpha
+
 include trackDb.encode3.ra
 
 include trackDb.transMap.ra
 
 include trackDb.nt.ra
 include trackDb.genbank.ra 
 include uniprot.ra
 
 include jaspar.ra
 
 include evaSnp.ra
 
 # Root trackDb.ra file.  Files from the organism subdirectory and the database sub-sub directory
 # will be layered on.  Organism is something like 'human' and database is something
 # like 'hg18'.  See the README file in this directory for a description of the format.
@@ -237,66 +240,30 @@
 shortLabel Duplications
 longLabel Duplications of >1000 Bases Sequence
 group map
 visibility hide
 type bed 6 +
 color 170,0,0
 altColor 160,150,0
 
 track dupes
 shortLabel Duplications
 longLabel Duplications of >98% Identity >1kb
 group map
 visibility dense
 type bed 6 .
 
-track altSeqLiftOverPsl
-shortLabel Alt Haplotypes
-longLabel Reference Assembly Alternate Haplotype Sequence Alignments
-group map
-type psl
-indelDoubleInsert on
-indelQueryInsert on
-showDiffBasesAllScales .
-showDiffBasesMaxZoom 10000.0
-showCdsMaxZoom 10000.0
-showCdsAllScales .
-baseColorDefault diffBases
-baseColorUseSequence db
-color 0,0,100
-visibility pack
-pennantIcon p14 black https://genome-blog.gi.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p14 patch sequences"
-
-track fixSeqLiftOverPsl
-shortLabel Fix Patches
-longLabel Reference Assembly Fix Patch Sequence Alignments
-group map
-type psl
-indelDoubleInsert on
-indelQueryInsert on
-showDiffBasesAllScales .
-showDiffBasesMaxZoom 10000.0
-showCdsMaxZoom 10000.0
-showCdsAllScales .
-baseColorDefault diffBases
-baseColorUseSequence db
-color 231,203,21
-darkerLabels on
-priority 1
-visibility pack
-pennantIcon p14 black https://genome-blog.gi.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p14 patch sequences"
-
 track knownAlt
 shortLabel UCSC Alt Events
 longLabel Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
 group genes
 visibility hide
 color 90,0,150
 noScoreFilter .
 type bed 6 .
 
 track ccdsGene
 shortLabel CCDS
 longLabel Consensus CDS
 group genes
 visibility hide
 color 12,120,12