03ee259959abfcc6dac85900579502fca9f803e5
chmalee
  Tue Mar 31 16:22:43 2020 -0700
Fix up mouseovers and filter labels for gnomad structural variants, and add a filter based on variant size, refs #24179

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 412f340..053d9bf 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -34223,48 +34223,48 @@
 #real    1m41.773s
     hgLoadChain hg19 -tIndex chainHg38ReMapAxtChain remap.axtChain.hg19.hg38.chain
 #Loading 2141 chains into hg19.chainHg38ReMapAxtChain
 
 
 ##############################################################################
 # gnomAD Structural Variants v2.1 - ChrisL
 # Redmine #24179
 
     cd /hive/data/outside/gnomAD.2/
     mkdir structuralVariants
 
     gsutil cp gs://gnomad-public/papers/2019-sv/gnomad_v2.1_sv.*.bed* .
     gsutil cp gs://gnomad-public/papers/2019-sv/gnomad_v2.1_sv.*.vcf* .
 
-    for f in *.bed.gz; do out=${f/.bed.gz/}; zcat $f | tail -n +2 | cut -f1-4,32 | tawk '{$1="chr"$1; print $0}'> $out.bed4Plus; done
+    for f in *.bed.gz; do out=${f/.bed.gz/}; zcat $f | tail -n +2 | cut -f1-4,18-28,31,32,36-38,41-42 | tawk '{$1="chr"$1; print $0}'> $out.bed4Plus; done
     # variant types:
     zcat gnomad_v2.1_sv.sites.bed.gz | cut -f32 | sort | uniq -c       
       52604 BND y
        4778 CPX x 
           8 CTX y
      169635 DEL x 
       49571 DUP x 
      109025 INS x 
         748 INV x 
        1108 MCNV x
           1 SVTYPE
 
     # add colors based on gnomad website and get in to proper bed9+
     for f in *.bed4Plus; do out=${f/.bed4Plus/}; bedClip -truncate $f $chromSizes stdout | ./gnomadSvToUcsc.awk | sort -k1,1 -k2,2n > $out.bed9Plus; done
 
     chromSizes=/hive/data/genomes/hg19/chrom.sizes
-    for f in *.bed9Plus; do out=${f/.bed9Plus/}; bedToBigBed -tab -type=bed9+1 -as=gnomadSv.as $f $chromSizes $out.bb; done
+    for f in *.bed9Plus; do out=${f/.bed9Plus/}; bedToBigBed -tab -type=bed9+19 -as=gnomadSv.as -extraIndex=name $f $chromSizes $out.bb; done
     mkdir -p /gbdb/hg19/gnomAD/structuralVariants/ 
     cd /gbdb/hg19/gnomAD/structuralVariants/
     cp -s /hive/data/outside/gnomAD.2/structuralVariants/*.bb .
 
 ##############################################################################
 2020-03-11: import of UCSC GENCODE group processing of GENCODE V34lift37 pre-release (markd)
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
 
     # download, build and load tables
     mkdir -p /hive/data/genomes/hg19/bed/gencodeV34lift37Pre
     pushd /hive/data/genomes/hg19/bed/gencodeV34lift37Pre
     (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
 
     # compare tables from previous release to see if number changed makes
     # sense.  Results are in gencode-cmp.tsv