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/patchTracks.new.ra src/hg/makeDb/trackDb/patchTracks.new.ra
new file mode 100644
index 00000000000..27648dd1669
--- /dev/null
+++ src/hg/makeDb/trackDb/patchTracks.new.ra
@@ -0,0 +1,47 @@
+track patchesPsl
+shortLabel GRC Patches
+longLabel GRC Patches: Alt Haplotypes and Fix Sequences
+compositeTrack on
+hideEmptySubtracks on
+group map
+visibility pack
+type psl
+html patchesPsl
+
+track altSeqLiftOverPsl
+parent patchesPsl
+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
+parent patchesPsl
+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"