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
@@ -1,186 +1,198 @@
 #!/bin/sh -ex
 
 pairRefDb=$1
 pairRefSeq=$2
 pairRefDb2bit=$3
 pairQueryDb=$4
 pairQuerySeq=$5
 pairQueryDb2bit=$6
 pairChain=$7
 
 filterChain=$pairRefSeq.$pairQuerySeq.$pairChain
 
 chainFilter -t=$pairRefSeq -q=$pairQuerySeq $pairChain > $filterChain
 
 buildPairAssembly $filterChain $pairRefSeq $pairRefDb2bit $pairQuerySeq $pairQueryDb2bit out.fa query.psl target.psl map.bed dup.bed miss.bed baseTarget.bed baseQuery.bed
 
 
 rm -rf hub
 mkdir hub
 
 faToTwoBit out.fa hub/buildPair.2bit
 twoBitInfo hub/buildPair.2bit hub/buildPair.sizes.txt
 bedToBigBed  -type=bed9+4 map.bed hub/buildPair.sizes.txt hub/map.bb
 
 axtChain -psl -linearGap=medium query.psl hub/buildPair.2bit $pairQueryDb2bit query.chain
 hgLoadChain -noBin -test hg38 bigChain  query.chain
 sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > query.bigChain
 bedToBigBed -type=bed6+6 -as=$HOME/kent/src/hg/lib/bigChain.as -tab query.bigChain  hub/buildPair.sizes.txt hub/queryChain.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/queryChain.link.bb
 
 axtChain -psl -linearGap=medium target.psl hub/buildPair.2bit $pairRefDb2bit target.chain
 hgLoadChain -noBin -test hg38 bigChain  target.chain
 sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > targetChain.bigChain
 bedToBigBed -type=bed6+6 -as=$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
 name map
 label Mapping
 priority 2
 defaultIsClosed 0
 
 name target
 label From $pairRefDb
 priority 3
 defaultIsClosed 0
 
 name query
 label From $pairQueryDb
 priority 3
 defaultIsClosed 0
 _EOF_
 
 cat << _EOF_ > hub/hub.txt
 hub buildPair
 longLabel buildPair
 email braney@ucsc.edu
 shortLabel buildPair
 useOneFile on
 
 genome $pairRefSeq-$pairQuerySeq
 defaultPos buildPair:1-20000
 organism $pairRefDb-$pairQueryDb
 twoBitPath buildPair.2bit
 groups groups.txt
 
 track map
 type bigBed 9
 bigDataUrl map.bb
 shortLabel Origin
 longLabel Origin
 itemRgb on
 group map
 
 track queryChain
 type bigChain $pairQueryDb
 bigDataUrl queryChain.bb
 shortLabel $pairQueryDb Alignment
 longLabel  $pairQueryDb Alignment
 group map
 
 track targetChain
 type bigChain $pairRefDb
 bigDataUrl targetChain.bb
 shortLabel $pairRefDb Alignment
 longLabel  $pairRefDb Alignment
 group map
 
 track ncbiRefSeqInsta
 searchIndex name
 color 12,12,120
 altColor 120,12,12
 shortLabel RefSeq All
 type bigGenePred
 bigDataUrl  /gbdb/hg38/ncbiRefSeq/ncbiRefSeq.bb
 longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*,
  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
 #group target
 
 track qrmsk
 type bigBed 9
 itemRgb on
 shortLabel Rmsk
 longLabel $pairQueryDb Rmsk
 bigDataUrl $rmskBb
 quickLiftUrl queryChain.bb
 group query
 
 track qsimple
 type bigBed 12
 shortLabel simpleRepeat
 longLabel $pairQueryDb simpleRepeat
 bigDataUrl $simpleBb
 quickLiftUrl queryChain.bb
 group query
 
 track ensGeneQuery
 type bigGenePred
 shortLabel Ensembl
 longLabel Ensembl
 bigDataUrl $ensGeneBb
 quickLiftUrl queryChain.bb
 group query
 
 _EOF_