03045b074b65d33e4893d9b4b2b464271f659a69
chmalee
  Fri Jan 8 14:43:10 2021 -0800
Forgot the cds and fa arguments to pslToBigPsl for lrg otto build, refs #24672

diff --git src/hg/utils/otto/lrg/buildLrg.sh src/hg/utils/otto/lrg/buildLrg.sh
index 0cbc130..7c42c7d 100755
--- src/hg/utils/otto/lrg/buildLrg.sh
+++ src/hg/utils/otto/lrg/buildLrg.sh
@@ -35,31 +35,32 @@
     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
 
     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"
     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
-    pslToBigPsl lrgTranscripts${db}.psl bigPsl.txt
+    awk '{printf ">%s\n%s\n", $1,$2}' lrgCdna.tab > lrgCdna.fa
+    pslToBigPsl -cds=lrgTranscripts.cds -fa=lrgCdna.fa lrgTranscripts${db}.psl bigPsl.txt
     join -t$'\t' -1 4 \
         -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15\
 ,1.16,1.17,1.18,1.19,1.20,1.21,1.22,1.23,1.24,1.25,2.2,2.3,2.4,2.5,2.6,2.7\
         <(sort -k4 bigPsl.txt) lrgTransExtraFields.tsv \
         | sort -k1,1 -k2,2n > lrgExtraTranscripts${db}.bigPsl.bed
 
     printf "Creating lrgBigPsl.bb for %s\n" $db
     bedToBigBed -as=${WORKDIR}/bigPsl+6.as -type=bed12+19 -tab \
         lrgExtraTranscripts${db}.bigPsl.bed /hive/data/genomes/${db}/chrom.sizes lrgBigPsl.bb
 
     # The lrg table already exists as a one line table pointing to /gbdb/$db/bbi/lrg.bb, which
     # is in turn a symlink into $WORKDIR/release/$db/lrg.bb. Thus validate now before overwriting:
     oldCount=`bigBedInfo ${WORKDIR}/release/$db/lrg.bb | grep itemCount | cut -d' ' -f2`
     oldPslCount=`bigBedInfo ${WORKDIR}/release/$db/lrgBigPsl.bb | grep itemCount | cut -d' ' -f2`
     newCount=`bigBedInfo lrg.bb | grep itemCount | cut -d' ' -f2`