c67f70fced286da481cf4a3c73013d1d2fca909b
max
  Fri Jul 1 07:07:13 2022 -0700
adding lrg ncbi accession to search specs, refs #29689

diff --git src/hg/utils/otto/lrg/buildLrg.sh src/hg/utils/otto/lrg/buildLrg.sh
index 24addf0..8b3503b 100755
--- src/hg/utils/otto/lrg/buildLrg.sh
+++ src/hg/utils/otto/lrg/buildLrg.sh
@@ -24,31 +24,31 @@
     # use -gt 1 because one of the lines will be the "checked: X, failed: Y" line
     if [ `grep -v "LRG_7t1\|LRG_1298t1" genePred.failed | wc -l` -gt 2 ]; then
         printf "genePredCheck failed on %s. Check %s for more info\n" "${db}" "${WORKDIR}/${today}/${db}/genePred.failed"
         exit 255
     fi
     cut -f1,12 lrgTranscriptsUnmapped.gp | sort > transcript.gene.name.txt
 
     awk -F$'\t' '{printf "%s\t%s\t%s\t%s\t%s\t%s\t%s %s %s %s\n", $1,$16,$17,$18,$19,$2, $16,$18,$17,$19}' \
         lrgTranscriptsUnmapped.gp | sort \
         | join -t$'\t' - transcript.gene.name.txt \
         | awk -F$'\t' '{printf "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s %s\n", $1,$2,$3,$4,$5,$6,$8,$7,$8}' \
         > lrgTransExtraFields.tsv
 
     printf "Creating lrg.bb for %s\n" $db
     bedToBigBed lrg.bed /hive/data/genomes/$db/chrom.sizes lrg.bb \
-        -tab -type=bed12+ -as=$HOME/kent/src/hg/lib/lrg.as -extraIndex=name
+        -tab -type=bed12+ -as=$HOME/kent/src/hg/lib/lrg.as -extraIndex=name,ncbiAcc
 
     ~/bin/x86_64/lrgToPsl lrg.bed /hive/data/genomes/$db/chrom.sizes lrg.psl
     set +e
     pslCheck -fail=lrg.psl.failed lrg.psl
     if [ `wc -l lrg.psl.failed | cut -d' ' -f1` -gt 0 ]; then
         printf "pslCheck failed for %s. Check %s for more info\n" "${db}" "${WORKDIR}/${today}/${db}/lrg.psl.failed"
         exit 255
     fi
     set -e
     awk '{print $10 "\t" $11;}' lrg.psl > lrg.sizes
     genePredToFakePsl -chromSize=lrg.sizes placeholder \
         lrgTranscriptsUnmapped.gp lrgTranscriptsFakePsl.psl lrgTranscripts.cds
     pslMap lrgTranscriptsFakePsl.psl lrg.psl lrgTranscripts${db}.psl
     awk '{printf ">%s\n%s\n", $1,$2}' lrgCdna.tab > lrgCdna.fa
     pslToBigPsl -cds=lrgTranscripts.cds -fa=lrgCdna.fa lrgTranscripts${db}.psl bigPsl.txt