df6cf391270cbbfe12f9ec3869948c2813002a87
braney
  Thu May 23 13:47:45 2024 -0700
add support for baseView track type

diff --git src/hg/utils/buildPairAssembly/makePair src/hg/utils/buildPairAssembly/makePair
index 9c92f70..aa96a71 100755
--- src/hg/utils/buildPairAssembly/makePair
+++ src/hg/utils/buildPairAssembly/makePair
@@ -35,30 +35,32 @@
 bedToBigBed -type=bed6+6 -as=$HOME/kent/src/hg/lib/bigChain.as -tab targetChain.bigChain  hub/buildPair.sizes.txt hub/targetChain.bb
 awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n > bigChain.bigLink
 bedToBigBed -type=bed4+1 -as=$HOME/kent/src/hg/lib/bigLink.as -tab bigChain.bigLink hub/buildPair.sizes.txt hub/targetChain.link.bb
 
 chainSwap query.chain swap.query.chain
 chainSwap target.chain swap.target.chain
 awk '{print $1,$2,$3,$7}' dup.bed | liftOver -minMatch=0.001 stdin swap.query.chain tmp foo
 awk '{print $4,$5,$6,$7}' dup.bed | liftOver -minMatch=0.001 stdin swap.target.chain tmp2 foo
 sort tmp tmp2 > tmp3
 bedToBigBed -type=bed4 -tab tmp3 hub/buildPair.sizes.txt hub/dups.bb
 
 bedToBigBed -type=bed4 miss.bed hub/buildPair.sizes.txt hub/mismatch.bb
 
 bedToBigBed -type=bed4+1 baseTarget.bed hub/buildPair.sizes.txt hub/baseTarget.bb
 
+bedToBigBed -type=bed4+1 baseQuery.bed hub/buildPair.sizes.txt hub/baseQuery.bb
+
 genome=$pairQueryDb
 gcX="${genome:0:3}"
 d0="${genome:4:3}"
 d1="${genome:7:3}"
 d2="${genome:10:3}"
 
 tmp=`cd /usr/local/apache/htdocs/hubs; echo $gcX/$d0/$d1/$d2/$genome/bbi/*ens*.bb `
 ensGeneBb=https://hgdownload.soe.ucsc.edu/hubs/$tmp
 tmp=`cd /usr/local/apache/htdocs/hubs; echo $gcX/$d0/$d1/$d2/$genome/bbi/*rmsk.bb `
 rmskBb=https://hgdownload.soe.ucsc.edu/hubs/$tmp
 tmp=`cd /usr/local/apache/htdocs/hubs; echo $gcX/$d0/$d1/$d2/$genome/bbi/*simpleRepeat.bb `
 simpleBb=https://hgdownload.soe.ucsc.edu/hubs/$tmp
 
 
 cat << _EOF_ > hub/groups.txt
@@ -124,35 +126,45 @@
  NP_* or YP_*)
 baseColorUseCds given
 baseColorDefault genomicCodons
 priority 1
 quickLiftUrl targetChain.bb
 canPack 1
 group target
 
 track qdups
 type bigBed 4
 bigDataUrl dups.bb
 shortLabel $pairQueryDb Dups
 longLabel  $pairQueryDb Dups
 group map
 
+track baseQuery
+priority 0.1
+type bigBaseView
+bigDataUrl baseQuery.bb
+shortLabel BaseView
+longLabel $pairQueryDb BaseView
+group query
+
 track baseTarget
-type bigBed 4
+priority 0.1
+type bigBaseView
 bigDataUrl baseTarget.bb
-shortLabel baseTarget
-longLabel baseTarget
+shortLabel BaseView
+longLabel $pairRefDb BaseView
+group target
 
 track mismatch
 type bigBed 4
 bigDataUrl mismatch.bb
 shortLabel Mismatches
 longLabel Mismatches between $pairRefDb and $pairQueryDb
 group map
 
 #track trmsk
 #type bigBed 9
 #itemRgb on
 #shortLabel Rmsk
 #longLabel $pairRefDb Rmsk
 #bigDataUrl $rmskBb
 #quickLiftUrl targetChain.bb