643e7a97358b25e2180c4dbfc64ff4aa2bb6e85d
markd
  Mon Apr 8 20:28:52 2024 -0700
rebuild hg38.chromAlias.bb

diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt
index 15bdfdf..785751c 100644
--- src/hg/makeDb/doc/hg38/hg38.txt
+++ src/hg/makeDb/doc/hg38/hg38.txt
@@ -7356,15 +7356,25 @@
     sed -e 's/^/    # /;' fb.GCF_009762305.2.chainSynHg38Link.txt
     # 1457122207 bases of 2409685272 (60.469%) in intersection
 \    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
     \
    -target2bit="/hive/data/genomes/asmHubs/GCF/009/762/305/GCF_009762305.2/GCF_009762305.2.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCF/009/762/305/GCF_009762305.2/GCF_009762305.2.chrom.sizes.txt" \
    GCF_009762305.2 hg38) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real      286m31.189s
 
     sed -e 's/^/    # /;' fb.GCF_009762305.2.chainRBest.Hg38.txt
     # 1461710350 bases of 2409685272 (60.660%) in intersection
 
 ##############################################################################
+# hg38.chromAlias.bb was incorrectly built without indexes so it will not
+# work with bedToBigBed 2024-04-08 markd
+
+cd /hive/data/genomes/hg38/goldenPath/bigZips/initial
+mv hg38.chromAlias.bb  hg38.chromAlias.noindexes.bb
+bigBedInfo -asOut hg38.chromAlias.noindexes.bb >hg38.chromAlias.as
+bigBedToBed hg38.chromAlias.noindexes.bb  hg38.chromAlias.bed
+bedToBigBed -tab -type=bed3+ -as=hg38.chromAlias.as hg38.chromAlias.bed -sizesIs2Bit  -extraIndex=ucsc,assembly,ensembl,genbank,refseq hg38.2bit hg38.chromAlias.bb
+
+##############################################################################