3442f799e4ddde42dfc0257e514ea1831a514f97
markd
  Sun Apr 24 21:03:28 2022 -0700
add score to T2T supplied liftOver chains

diff --git src/hg/makeDb/doc/chm13v2.0userData/build.txt src/hg/makeDb/doc/chm13v2.0userData/build.txt
index 57fe414..179dce6 100644
--- src/hg/makeDb/doc/chm13v2.0userData/build.txt
+++ src/hg/makeDb/doc/chm13v2.0userData/build.txt
@@ -130,64 +130,64 @@
     chm13v2-hg19_chrM.chain
     chm13v2-hg19_chrMT.chain
     hg19_chrM-chm13v2.chain
     hg19_chrMT-chm13v2.chain
 
    cd trackData/hgLiftOver
 
 # rename to match UCSC conventions
     mv chm13v2-grch38.chain chm13v2-hg38.over.no-id.chain
     mv grch38-chm13v2.chain hg38-chm13v2.over.no-id.chain
     mv chm13v2-hg19_chrM.chain chm13v2-hg19_chrM.over.no-id.chain
     mv chm13v2-hg19_chrMT.chain chm13v2-hg19_chrMT.over.no-id.chain
     mv hg19_chrM-chm13v2.chain hg19_chrM-chm13v2.over.no-id.chain
     mv hg19_chrMT-chm13v2.chain  hg19_chrMT-chm13v2.over.no-id.chain
 
-# add chain ids
-    chainMergeSort chm13v2-hg19_chrM.over.no-id.chain   > chm13v2-hg19_chrM.over.chain     
-    chainMergeSort chm13v2-hg19_chrMT.over.no-id.chain  > chm13v2-hg19_chrMT.over.chain    
-    chainMergeSort chm13v2-hg19.over.no-id.chain        > chm13v2-hg19.over.chain          
-    chainMergeSort chm13v2-hg38.over.no-id.chain        > chm13v2-hg38.over.chain          
-    chainMergeSort hg19-chm13v2.over.no-id.chain        > hg19-chm13v2.over.chain          
-    chainMergeSort hg19_chrM-chm13v2.over.no-id.chain   > hg19_chrM-chm13v2.over.chain     
-    chainMergeSort hg19_chrMT-chm13v2.over.no-id.chain  > hg19_chrMT-chm13v2.over.chain    
+# add chain ids and score
+    chainMergeSort chm13v2-hg19_chrM.over.no-id.chain | chainScore stdin ../ucscChromNames/t2t-chm13-v2.0.2bit /hive/data/genomes/hg19/hg19.2bit chm13v2-hg19_chrM.over.chain     
+    chainMergeSort chm13v2-hg19_chrMT.over.no-id.chain | chainScore stdin ../ucscChromNames/t2t-chm13-v2.0.2bit /hive/data/genomes/hg19/hg19.2bit chm13v2-hg19_chrMT.over.chain    
+    chainMergeSort chm13v2-hg38.over.no-id.chain | chainScore stdin ../ucscChromNames/t2t-chm13-v2.0.2bit /hive/data/genomes/hg38/hg38.2bit chm13v2-hg38.over.chain
+
+    chainMergeSort hg19_chrM-chm13v2.over.no-id.chain | chainScore stdin /hive/data/genomes/hg19/hg19.2bit ../ucscChromNames/t2t-chm13-v2.0.2bit hg19_chrM-chm13v2.over.chain     
+    chainMergeSort hg19_chrMT-chm13v2.over.no-id.chain  | chainScore stdin /hive/data/genomes/hg19/hg19.2bit ../ucscChromNames/t2t-chm13-v2.0.2bit  hg19_chrMT-chm13v2.over.chain    
+
     chainMergeSort hg38-chm13v2.over.no-id.chain         > hg38-chm13v2.over.chain          
 
 
 # create hg19 chains that combine chrM and chrMT for use in browser.
    chainFilter -q=chrMT chm13v2-hg19_chrMT.over.chain | chainMergeSort stdin chm13v2-hg19_chrM.over.chain > chm13v2-hg19.over.chain
    chainFilter -t=chrMT hg19_chrMT-chm13v2.over.chain | chainMergeSort stdin  hg19_chrM-chm13v2.over.chain > hg19-chm13v2.over.chain
 
    pigz *.chain
 
 # build tracks
     hgLoadChain -noBin -test none bigChain chm13v2-hg38.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 ../chromAlias/ucsc.sizes.txt chm13v2-hg38.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 ../chromAlias/ucsc.sizes.txt chm13v2-hg38.over.link.bb
 
     hgLoadChain -noBin -test none bigChain chm13v2-hg19.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 ../chromAlias/ucsc.sizes.txt chm13v2-hg19.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 ../chromAlias/ucsc.sizes.txt chm13v2-hg19.over.link.bb
 
     rm *.tab
 
    # make available is liftOver directory as we
-   ln -f *.chain.gz ../../liftOver/
+   ln -f *.over.chain.gz ../../liftOver/
 
 # GRCh38 mask used in liftover. This is based on:
 #  https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_GRC_exclusions_T2Tv2.bed
 #  plus UCSC hg38 centromeres track
 
    GRCh38: /team-liftover/grch38_masked_fasta/grch38-centromere_and_falsedup.bed (edited)
    rename to hg38.liftover-mask.bed
    ln -f hg38.liftover-mask.bed ../../liftOver/
 
 
 ================================================================
 * hgCactus (2022-03-28 markd)
 ----------------------------------------------------------------
 # HAL from Marina Haukness <mhauknes@ucsc.edu>