97199fbf1ff56c9ee01956deb736b97244ea3ac6
hiram
  Sun Mar 1 21:52:28 2020 -0800
calculating featureBits like measurement for gene tracks, removing duplicates for ncbiRefSeq, remove blanks from gene names for ncbiRefSeq, and fix fundamental bug reference to geneToId in ncbiRefSeqOtherAttrs.pl refs #23891

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index bd3e7fb..0534908 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1499,31 +1499,31 @@
         | gzip -c > \$asmId.ncbiGene.genePred.gz
   genePredCheck \$asmId.ncbiGene.genePred.gz
   export howMany=`genePredCheck \$asmId.ncbiGene.genePred.gz 2>&1 | grep "^checked" | awk '{print \$2}'`
   if [ "\${howMany}" -eq 0 ]; then
      printf "# ncbiGene: no gene definitions found in \$gffFile\n";
      cleanUp
      exit 0
   fi
   liftUp -extGenePred -type=.gp stdout \\
       ../../sequence/\$asmId.ncbiToUcsc.lift warn \\
        \$asmId.ncbiGene.genePred.gz | gzip -c \\
           > \$asmId.ncbiGene.ucsc.genePred.gz
   genePredToBed -tab -fillSpace \$asmId.ncbiGene.ucsc.genePred.gz stdout \\
     | bedToExons stdin stdout | bedSingleCover.pl stdin > \$asmId.exons.bed
   export baseCount=`awk '{sum+=\$3-\$2}END{printf "%d", sum}' \$asmId.exons.bed`
-  export asmSizeNoGaps=`grep sequences ../../\$asmId.faSize.txt | awk '{print \$1}'`
+  export asmSizeNoGaps=`grep sequences ../../\$asmId.faSize.txt | awk '{print \$5}'`
   export perCent=`echo \$baseCount \$asmSizeNoGaps | awk '{printf "%.3f", 100.0*\$1/\$2}'`
   rm -f \$asmId.exons.bed
   ~/kent/src/hg/utils/automation/gpToIx.pl \$asmId.ncbiGene.ucsc.genePred.gz \\
     | sort -u > \$asmId.ncbiGene.ix.txt
   ixIxx \$asmId.ncbiGene.ix.txt \$asmId.ncbiGene.ix \$asmId.ncbiGene.ixx
   rm -f \$asmId.ncbiGene.ix.txt
   genePredToBigGenePred \$asmId.ncbiGene.ucsc.genePred.gz stdout \\
       | sort -k1,1 -k2,2n > \$asmId.ncbiGene.bed
   (bedToBigBed -type=bed12+8 -tab -as=\$HOME/kent/src/hg/lib/bigGenePred.as \\
       -extraIndex=name \$asmId.ncbiGene.bed \\
         ../../\$asmId.chrom.sizes \$asmId.ncbiGene.bb || true)
   if [ ! -s "\$asmId.ncbiGene.bb" ]; then
     printf "# ncbiGene: failing bedToBigBed\\n" 1>&2
     exit 255
   fi