9160ba77561829b8e213058680623b63d35262dc
braney
  Fri Sep 3 10:40:47 2021 -0700
get synBlast to work with bigBed

diff --git src/hg/utils/automation/synBlastp.csh src/hg/utils/automation/synBlastp.csh
index 7a04062..d7627e4 100755
--- src/hg/utils/automation/synBlastp.csh
+++ src/hg/utils/automation/synBlastp.csh
@@ -122,31 +122,31 @@
 
 
 # --- filter $db.xxBlastTab based on pslMapped $db.kg hgMapToGene'd over to $otherDb.kg ---
 
 echo "genePredToFakePsl:"
 genePredToFakePsl $db $geneTable $db.kg.psl $db.kg.cds
 
 echo "pslMap via $lift :"
 zcat $lift | pslMap -chainMapFile -swapMap $db.kg.psl stdin stdout \
 |  sort -k 14,14 -k 16,16n > $db.$otherDb.kg.psl
 
 echo "hgLoadPsl:"
 hgLoadPsl -clientLoad $otherDb $db.$otherDb.kg.psl -table=temp${db}KgPslMapped
 
 echo "hgMapToGene:"
-hgMapToGene -all $otherDb -type=psl -verbose=0 temp${db}KgPslMapped $otherGeneTable temp${otherDb}kgTo${db}kg
+hgMapToGene  -geneTableType=genePred  -all $otherDb -type=psl -verbose=0 temp${db}KgPslMapped $otherGeneTable temp${otherDb}kgTo${db}kg
 
 echo "$db.${xxBlastTab}:"
 
 # original for comparison:
 set sql = "select count(distinct query) from ${xxBlastTab}"; echo "old number of unique query values:"; hgsql $db -BN -e "$sql"
 set sql = "select count(distinct target) from ${xxBlastTab}"; echo "old number of unique target values"; hgsql $db -BN -e "$sql"
 
 # drop rows that do not have a match in the psl-mapped otherDb table.
 hgsql $db -BN -e "delete a from ${xxBlastTab} a left join ${otherDb}.temp${otherDb}kgTo${db}kg b on (a.query = b.value and a.target = b.name) where b.value is NULL"
 
 set sql = "select count(distinct query) from ${xxBlastTab}"; echo "new number of unique query values:"; hgsql $db -BN -e "$sql"
 set sql = "select count(distinct target) from ${xxBlastTab}"; echo "new number of unique target values"; hgsql $db -BN -e "$sql"
 
 #cleanup: