eb5f674d8ebadc542e4fbad84e465a629bdee6c7
hiram
  Thu Oct 15 09:17:33 2020 -0700
correctly create near mis list refs #24547

diff --git src/hg/makeDb/doc/assemblyEquivalence/A.vs.B.sh src/hg/makeDb/doc/assemblyEquivalence/A.vs.B.sh
index a5c73ab..f58bcbe 100755
--- src/hg/makeDb/doc/assemblyEquivalence/A.vs.B.sh
+++ src/hg/makeDb/doc/assemblyEquivalence/A.vs.B.sh
@@ -1,46 +1,45 @@
 #!/bin/bash
 
 if [ $# -ne 2 ]; then
   printf "usage: ./A.vs.B.sh <a> <b>\n" 1>&2
   printf "where <a> <b> is a pair from:\n" 1>&2
   printf "ucsc, genbank, refseq, ensembl\n" 1>&2
   printf "creates files: nearMiss.a.b.run.list nearMiss.b.a.run.list\n" 1>&2
   exit 255
 fi
 
 export A=$1
 export B=$2
 
 printf "# existing list size:\n"
 wc -l nearMiss.${A}.${B}.run.list nearMiss.${B}.${A}.run.list
 
 cut -f1 ../${A}.${B}.exact.txt | sort -u > ${A}.${B}.done.list
 cut -f1 ../${B}.${A}.exact.txt | sort -u > ${B}.${A}.done.list
 
 cut -f2 ../${B}/${B}.keySignatures.txt  | sort -u > ${B}.full.list
 cut -f2 ../${A}/${A}.keySignatures.txt  | sort -u > ${A}.full.list
 
 comm -13 ${B}.${A}.done.list ${B}.full.list > ${B}.${A}.toMatch.list
 comm -13 ${A}.${B}.done.list ${A}.full.list > ${A}.${B}.toMatch.list
 
 join -t$'\t' -2 2 ${B}.${A}.toMatch.list \
     <(sort -k2,2 ../${B}/${B}.keySignatures.txt) \
       | awk '{printf "%d\t%s\t%d\n", $4,$1,$3}' | sort -n \
          > uniqueCounts.${B}.${A}.txt
 
 join -t$'\t' -2 2 ${A}.${B}.toMatch.list \
   <(sort -k2,2 ../${A}/${A}.keySignatures.txt) \
       | awk '{printf "%d\t%s\t%d\n", $4,$1,$3}' | sort -n \
          > uniqueCounts.${A}.${B}.txt
 
-/cluster/home/hiram/kent/src/hg/makeDb/doc/assemblyEquivalence
 ~/kent/src/hg/makeDb/doc/assemblyEquivalence/createNearMissRunList.pl 10 \
    uniqueCounts.${B}.${A}.txt uniqueCounts.${A}.${B}.txt \
      > nearMiss.${A}.${B}.run.list
 
 ~/kent/src/hg/makeDb/doc/assemblyEquivalence/createNearMissRunList.pl 10 \
    uniqueCounts.${A}.${B}.txt uniqueCounts.${B}.${A}.txt \
      > nearMiss.${B}.${A}.run.list
 
 printf "# newly created list size:\n"
 wc -l nearMiss.${A}.${B}.run.list nearMiss.${B}.${A}.run.list