4dadcc59eac20a561ddc52cd71ac122813dabc32
markd
  Mon May 23 14:40:45 2022 -0700
change CHM13 repeatmasker to used bed9 itemRgb until bigRmsk bugs are sorted out (Track #29494)

diff --git src/hg/makeDb/doc/chm13v2.0userData/build.txt src/hg/makeDb/doc/chm13v2.0userData/build.txt
index 00aff7a..8559d9d 100644
--- src/hg/makeDb/doc/chm13v2.0userData/build.txt
+++ src/hg/makeDb/doc/chm13v2.0userData/build.txt
@@ -356,30 +356,36 @@
 
 # notes from Robert on how tracks were created:
     # Build trackHub tsv files from the combo* files:
     /home/rhubley/projects/RepeatMasker/util/rmToTrackHub2.pl \
       -out combo.out \
       -align combo.align
 
     # Sort tsv files
     sort -k1,1 -k2,2n  combo.join.tsv >  combo.join.tsv.sorted
     sort -k1,1 -k2,2n  combo.align.tsv >  combo.align.tsv.sorted
 
     # Convert to bigRmskBed and bigRmskAlignBed files
     /usr/local/ucscTools/bedToBigBed -tab -as=bigRmskAlignBed.as -type=bed3+14  combo.align.tsv.sorted chrom.sizes chm13v2.0_RMSK_ALIGN.bb
     /usr/local/ucscTools/bedToBigBed -tab -as=bigRmskBed.as -type=bed9+5 combo.join.tsv.sorted chrom.sizes chm13v2.0_RMSK.bb
 
+2022-05-23
+# due to the number of problems with the bigRmsk code, we are temporarily converting it to
+# a bigBed and added colors.
+
+  cd /hive/data/genomes/asmHubs/genbankBuild/GCA/009/914/755/GCA_009914755.4_T2T-CHM13v2.0/trackData/t2tRepeatMasker
+  bigBedToBed chm13v2.0_rmsk.align.bb stdout |  awk -f addItemRgb.awk >chm13v2.0_rmsk.align.rgb.bed
 
 
 ================================================================
 pending:
 
 - ensembl:
   http://ftp.ebi.ac.uk/pub/databases/ensembl/hprc/y1_freeze/ contains all Y1 assemblies;
   http://ftp.ebi.ac.uk/pub/databases/ensembl/hprc/y1_freeze/GCA_009914755.4/ is CHM13v2
 
 - isoseq BAMs
   http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/out-t2t-chrY-augPB/assemblyHub/CHM13/
   @PG   ID:minimap2   PN:minimap2   VN:2.22-r1105-dirty   CL:minimap2 -ax splice -f 1000 --sam-hit-only --secondary=no --eqx -K 100M -t 8 --cap-sw-mem=3g chm13v2.0.chrY.fasta HG002-NA24385-LCL-polished_isoforms_hq.fasta
   globus /HG002-IsoSeq
 
 - isoseq