a3daddc4cea89f18fa40b571bfc97d47ad01b0a8
hiram
  Tue Dec 6 17:40:27 2022 -0800
correct variable name no redmine

diff --git src/hg/utils/automation/asmHubRepeatMasker.sh src/hg/utils/automation/asmHubRepeatMasker.sh
index 99081f9..6e40ee0 100755
--- src/hg/utils/automation/asmHubRepeatMasker.sh
+++ src/hg/utils/automation/asmHubRepeatMasker.sh
@@ -1,144 +1,144 @@
 #!/bin/bash
 
 # asmHubRepeatMasker.sh - process a specified *.fa.out.gz file into a set
 #                         of bigBed files for assembly hub display
 #
 # fail on any error:
 set -beEu -o pipefail
 
 # ensure sort functions properly despite kluster node environment
 export LC_COLLATE=C
 
 if [ $# -ne 3 ]; then
   printf "%s\n" "usage: asmHubRepeatMasker.sh <asmId> <pathTo/*fa.out.gz> <destinationDir/>" 1>&2
   exit 255
 fi
 
 export dateStamp=`date "+%FT%T %s"`
 
 export asmId=$1
 export rmOutFile=$2
 export destDir=$3
 export chrSizes=""
 
 if [ -s "$destDir/$asmId.chrom.sizes" ]; then
   chrSizes="$destDir/$asmId.chrom.sizes"
-elif [ -s "../../$admId.chrom.sizes" ]; then
+elif [ -s "../../$asmId.chrom.sizes" ]; then
   chrSizes="../../$asmId.chrom.sizes"
 fi
 
 # assume this file name pattern
 export faAlign=`echo "${rmOutFile}" | sed -e 's/sorted.fa.out/fa.align/; s/.gz//;'`
 export RepeatMaskerPath="/hive/data/staging/data/RepeatMasker210401"
 
 if [ -d "${destDir}" ]; then
   cd "${destDir}"
 
   # might already be gzipped
   if [ ! -s "${faAlign}" ]; then
      faAlign="${faAlign}.gz"
   fi
   # align file only exists when RM has been run locally, not for NCBI version
   # it is OK if it is missing, can do this anyway without it
   if [ -s "${faAlign}" ]; then
     printf "$RepeatMaskerPath/util/rmToTrackHub.pl -out \"${rmOutFile}\" -align \"${faAlign}\"\n" 1>&2
     $RepeatMaskerPath/util/rmToTrackHub.pl -out "${rmOutFile}" -align "${faAlign}"
     # in place same file sort using the -o output option
     sort -k1,1 -k2,2n -o "${asmId}.fa.align.tsv" "${asmId}.fa.align.tsv" &
   else
     printf "$RepeatMaskerPath/util/rmToTrackHub.pl -out \"${rmOutFile}\"\n" 1>&2
     $RepeatMaskerPath/util/rmToTrackHub.pl -out "${rmOutFile}"
   fi
   sort -k1,1 -k2,2n -o "${asmId}.sorted.fa.join.tsv" "${asmId}.sorted.fa.join.tsv" &
   wait
   bedToBigBed -tab -as=$HOME/kent/src/hg/lib/bigRmskBed.as -type=bed9+5 \
     "${asmId}.sorted.fa.join.tsv" "${chrSizes}" \
       "${asmId}.rmsk.bb" &
   if [ -s "${asmId}.fa.align.tsv" ]; then
     bedToBigBed -tab -as=$HOME/kent/src/hg/lib/bigRmskAlignBed.as \
       -type=bed3+14 "${asmId}.fa.align.tsv" "${chrSizes}" \
         "${asmId}.rmsk.align.bb" &
   fi
   wait
   if [ -s "${asmId}.fa.align.tsv" ]; then
     gzip "${asmId}.fa.align.tsv" &
   fi
   gzip "${asmId}.sorted.fa.join.tsv" &
   wait
   rm -fr classBed rmskClass ${asmId}.rmsk.tab bbi/*.rmsk.*.bb \
        bbi/*.rmsk.*.bb
   mkdir classBed rmskClass
   rm -f ${asmId}.rm.out
   mkdir -p bbi
   dateStamp=`date "+%FT%T %s"`
   printf "# %s processing %s\n" "${dateStamp}" "${rmOutFile}" 1>&2
   export rmOutTmp=`mktemp -p /dev/shm rmskProcess.${asmId}.XXXXX`
   printf "%s\n" '   SW  perc perc perc  query      position in query           matching       repeat              position in  repeat
 score  div. del. ins.  sequence    begin     end    (left)    repeat         class/family         begin  end (left)   ID
 ' > "${rmOutTmp}"
   zcat "${rmOutFile}" | headRest 3 stdin >> "${rmOutTmp}"
   hgLoadOut -verbose=2 -tabFile=${asmId}.rmsk.tab -table=rmsk -nosplit test "${rmOutTmp}" 2> rmsk.bad.records.txt
   dateStamp=`date "+%FT%T %s"`
   if [ -s ${asmId}.rmsk.tab ]; then
     printf "# %s splitting into categories %s\n" "${dateStamp}" "${asmId}.rmsk.tab" 1>&2
     sort -k12,12 ${asmId}.rmsk.tab \
       | splitFileByColumn -ending=tab  -col=12 -tab stdin rmskClass
     for T in SINE LINE LTR DNA Simple Low_complexity Satellite
     do
       fileCount=`(ls rmskClass/${T}*.tab 2> /dev/null || true) | wc -l`
       if [ "$fileCount" -gt 0 ]; then
          dateStamp=`date "+%FT%T %s"`
          printf "# %s bedToBigBed on: rmskClass/%s*.tab " "${dateStamp}" "${T}"
          ls rmskClass/${T}*.tab | xargs echo
          $HOME/kent/src/hg/utils/automation/rmskBed6+10.pl rmskClass/${T}*.tab \
           | sort -k1,1 -k2,2n > classBed/${asmId}.rmsk.${T}.bed
        bedToBigBed -tab -type=bed6+10 -as=$HOME/kent/src/hg/lib/rmskBed6+10.as \
            classBed/${asmId}.rmsk.${T}.bed "${chrSizes}" \
              bbi/${asmId}.rmsk.${T}.bb &
       fi
     done
     wait
     fileCount=`(ls rmskClass/*RNA.tab 2> /dev/null || true) | wc -l`
     if [ "$fileCount" -gt 0 ]; then
       dateStamp=`date "+%FT%T %s"`
       printf "# %s bedToBigBed on rmskClass/*RNA.tab: " "${dateStamp}"
       ls rmskClass/*RNA.tab | xargs echo
       $HOME/kent/src/hg/utils/automation/rmskBed6+10.pl rmskClass/*RNA.tab \
          | sort -k1,1 -k2,2n > classBed/${asmId}.rmsk.RNA.bed
       bedToBigBed -tab -type=bed6+10 -as=$HOME/kent/src/hg/lib/rmskBed6+10.as \
          classBed/${asmId}.rmsk.RNA.bed "${chrSizes}" \
             bbi/${asmId}.rmsk.RNA.bb
     fi
     dateStamp=`date "+%FT%T %s"`
     printf "# %s checking ls rmskClass/*.tab | egrep -v \"/SIN|/LIN|/LT|/DN|/Simple|/Low_complexity|/Satellit|RNA.tab\" " "${dateStamp}"
     otherCount=`(ls rmskClass/*.tab 2> /dev/null || true) | (egrep -v "/SIN|/LIN|/LT|/DN|/Simple|/Low_complexity|/Satellit|RNA.tab" || true) | wc -l`
     if [ "${otherCount}" -gt 0 ]; then
       dateStamp=`date "+%FT%T %s"`
       printf "# %s bedToBigBed on: " "${dateStamp}"
       ls rmskClass/*.tab | egrep -v "/SIN|/LIN|/LT|/DN|/Simple|/Low_complexity|/Satellit|RNA.tab" | xargs echo | sed -e 's#rmskClass/##g;'
       $HOME/kent/src/hg/utils/automation/rmskBed6+10.pl `ls rmskClass/*.tab | egrep -v "/SIN|/LIN|/LT|/DN|/Simple|/Low_complexity|/Satellit|RNA.tab" | sed -e 's/^/"/; s/$/"/;'|xargs echo` \
           | sort -k1,1 -k2,2n > classBed/${asmId}.rmsk.Other.bed
       bedToBigBed -tab -type=bed6+10 -as=$HOME/kent/src/hg/lib/rmskBed6+10.as \
         classBed/${asmId}.rmsk.Other.bed "${chrSizes}" \
           bbi/${asmId}.rmsk.Other.bb
     fi
 
     export bbiCount=`for F in bbi/*.rmsk.*.bb; do bigBedInfo $F | grep itemCount; done | awk '{print $NF}' | sed -e 's/,//g' | ave stdin | grep total | awk '{print $2}' | sed -e 's/.000000//'`
 
     export firstTabCount=`cat ${asmId}.rmsk.tab | wc -l`
     export splitTabCount=`cat rmskClass/*.tab | wc -l`
 
     if [ "$firstTabCount" -ne $bbiCount ]; then
        printf "%s.rmsk.tab count: %d, split class tab file count: %d, bbi class item count: %d\n" "${asmId}" $firstTabCount $splitTabCount $bbiCount 1>&2
        printf "ERROR: did not account for all items in rmsk class bbi construction\n" 1>&2
        exit 255
     fi
     wc -l classBed/*.bed > ${asmId}.rmsk.class.profile.txt
     wc -l rmskClass/*.tab >> ${asmId}.rmsk.class.profile.txt
     rm -fr rmskClass classBed ${asmId}.rmsk.tab
   fi
   rm -f "${rmOutTmp}"
 else
   printf "ERROR: can not find destination directory '%s'\n" "${destDir}" 1>&2
   exit 255
 fi