2afb0b02aca7612ab8dc1bc6c7751eacd16f5c59
gperez2
  Thu Apr 3 09:32:12 2025 -0700
Adding Alignment Gap/Insertion Display settings for the GRC Patches composite track that are default in both Fix Patches and Alt Haplotypes track, refs #35326

diff --git src/hg/makeDb/trackDb/patchTracks.new.ra src/hg/makeDb/trackDb/patchTracks.new.ra
index 27648dd1669..d88d71349bd 100644
--- src/hg/makeDb/trackDb/patchTracks.new.ra
+++ src/hg/makeDb/trackDb/patchTracks.new.ra
@@ -1,47 +1,49 @@
 track patchesPsl
 shortLabel GRC Patches
 longLabel GRC Patches: Alt Haplotypes and Fix Sequences
 compositeTrack on
 hideEmptySubtracks on
 group map
 visibility pack
+indelDoubleInsert on
+indelQueryInsert on
 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"