7e49f8f7b02b41d0bab2051250a3a08ce4ffafd0
braney
  Fri May 17 11:45:39 2024 -0700
ongoing work on pairBrowser

diff --git src/hg/utils/buildPairAssembly/makePair src/hg/utils/buildPairAssembly/makePair
index 7769e87..5dad53e 100755
--- src/hg/utils/buildPairAssembly/makePair
+++ src/hg/utils/buildPairAssembly/makePair
@@ -1,85 +1,106 @@
 #!/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
+buildPairAssembly $filterChain $pairRefSeq $pairRefDb2bit $pairQuerySeq $pairQueryDb2bit out.fa query.psl target.psl map.bed dup.bed miss.bed
 
 
 rm -rf hub
 mkdir hub
 
 faToTwoBit out.fa hub/buildPair.2bit
 twoBitInfo hub/buildPair.2bit hub/buildPair.sizes.txt
-bedToBigBed  map.bed hub/buildPair.sizes.txt hub/map.bb
+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
+
+
 cat << _EOF_ > hub/hub.txt
 hub buildPair
 longLabel buildPair
 email braney@ucsc.edu
 shortLabel buildPair
 useOneFile on
 
 genome buildPair
 defaultPos buildPair:1-2
 organism buildPair
 twoBitPath buildPair.2bit
 
 track map
 type bigBed 9
 bigDataUrl map.bb
 shortLabel map
 longLabel map
 itemRgb on
 
 track queryChain
 type bigChain $pairQueryDb
 bigDataUrl queryChain.bb
 shortLabel queryChain
 longLabel queryChain
 
 track targetChain
 type bigChain $pairRefDb
 bigDataUrl targetChain.bb
 shortLabel targetChain
 longLabel targetChain
 
 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
-_EOF_
 
+track dups
+type bigBed 4
+bigDataUrl dups.bb
+shortLabel dups
+longLabel dups
+
+track mismatch
+type bigBed 4
+bigDataUrl mismatch.bb
+shortLabel mismatch
+longLabel mismatch
+_EOF_