f59b87d2038e90c7969da0fa0cc3652d41720881
markd
  Wed Mar 30 12:34:29 2022 -0700
create hg19/hg39 CHM13 liftover chains using NCBI names for now

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index db50aa3..2066151 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -34764,36 +34764,53 @@
 #############################################################################
 # chm13 liftover alignments  (2022-03-29 markd)
 
 # preliminary CHM13 <-> hg19 liftOver chains until NCBI produces consensus alignments
 # provide by Nae-Chyun Chen <naechyun.chen@gmail.com>
 
     mkdir -p /hive/data/genomes/hg19/bed/chm13LiftOver
     cd /hive/data/genomes/hg19/bed/chm13LiftOver
 
 # Obtain GRCh37 from T2T Globus: team-liftover/v1_nflo/grch37-chm13v2.chain
 
 # rename to better match UCSC convetions and compress
     mv grch37-chm13v2.chain hg19-chm13v2.over.chain
     pigz hg19-chm13v2.over.chain
 
+# make NCBI query names as well, since chromAlias doesn't work yet for click-through
+# note doc is wrong in chromToPsl PSL query is 10
+    chainToPslBasic hg19-chm13v2.over.chain.gz stdout | chromToUcsc -k 10 -a /hive/data/genomes/asmHubs/genbankBuild/GCA/009/914/755/GCA_009914755.4_CHM13_T2T_v2.0/GCA_009914755.4_CHM13_T2T_v2.0.chromAlias.txt | pslToChain stdin stdout | pigz -c > hg19-chm13v2.ncbi-qnames.over.chain.gz
+
 # build bigChain files:
     hgLoadChain -noBin -test none bigChain hg19-chm13v2.over.chain.gz 
     sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > bigChainIn.tab
     bedToBigBed -type=bed6+6 -as=${HOME}/kent/src/hg/lib/bigChain.as -tab bigChainIn.tab ../../chrom.sizes hg19-chm13v2.over.chain.bb
     tawk '{print $1, $2, $3, $5, $4}' link.tab | csort -k1,1 -k2,2n --parallel=64 > bigLinkIn.tab
     bedToBigBed -type=bed4+1 -as=${HOME}/kent/src/hg/lib/bigLink.as -tab bigLinkIn.tab  ../../chrom.sizes hg19-chm13v2.over.link.bb
 
+# build bigChain with NCBI names files:
+    hgLoadChain -noBin -test none bigChain hg19-chm13v2.ncbi-qnames.over.chain.gz 
+    sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > bigChainIn.tab
+    bedToBigBed -type=bed6+6 -as=${HOME}/kent/src/hg/lib/bigChain.as -tab bigChainIn.tab ../../chrom.sizes hg19-chm13v2.ncbi-qnames.over.chain.bb
+    tawk '{print $1, $2, $3, $5, $4}' link.tab | csort -k1,1 -k2,2n --parallel=64 > bigLinkIn.tab
+    bedToBigBed -type=bed4+1 -as=${HOME}/kent/src/hg/lib/bigLink.as -tab bigLinkIn.tab  ../../chrom.sizes hg19-chm13v2.ncbi-qnames.over.link.bb
+
+    rm *.tab
+   
 # link to gbdb
   mkdir -p /gbdb/hg19/bbi/chm13LiftOver
   ln -sf $(pwd)/*.bb /gbdb/hg19/bbi/chm13LiftOver/
 
 # make downloads, can't add to liftOver directory due to license in that directory
   mkdir -p /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/
-  ln -sf $(pwd)/hg19-chm13v2.over.chain.gz /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/
+  ln -sf $(pwd)/hg19-chm13v2.*.chain.gz /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/
   
 # push these files
+  /gbdb/hg19/bbi/chm13LiftOver/hg19-chm13v2.ncbi-qnames.over.chain.bb
+  /gbdb/hg19/bbi/chm13LiftOver/hg19-chm13v2.ncbi-qnames.over.link.bb
   /gbdb/hg19/bbi/chm13LiftOver/hg19-chm13v2.over.chain.bb
   /gbdb/hg19/bbi/chm13LiftOver/hg19-chm13v2.over.link.bb
+  /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/hg19-chm13v2.ncbi-qnames.over.chain.gz
   /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/hg19-chm13v2.over.chain.gz
 
-# NOTES: chromAlias doesn't work on click through yet, so disable for now
+  
+#############################################################################