2bdb4c4bf6c6b3525de22edaf18815061acd800b
chmalee
  Wed Jun 14 13:43:45 2023 -0700
Change highRepro bed track to a bigBed 9 so filters can work, refs #31122

diff --git src/hg/makeDb/doc/hg38/problematic.txt src/hg/makeDb/doc/hg38/problematic.txt
index 7b22557..be4a6c6 100644
--- src/hg/makeDb/doc/hg38/problematic.txt
+++ src/hg/makeDb/doc/hg38/problematic.txt
@@ -59,17 +59,17 @@
 chr1    13129   13367
 chr1    13520   13633
 ...
 
 # so turn those into bigBeds and link everything to /gbdb
 for f in $(ls *.bed); do base=$(basename -s .bed $f); bedSort ${f} ${f}.sorted; bedToBigBed ${f}.sorted../../../chrom.sizes ${base}.bb; done
 # for some reason tabix doesn't like to be run in a for loop from ls, needs find
 for f in $(find . -name "*.vcf.gz"); do tabix --verbosity 3 -p vcf "${f}"; done
 mkdir -p /gbdb/hg38/problematic/highRepro
 ln -s `pwd`/*.bb /gbdb/hg38/problematic/highRepro/
 ln -s `pwd`/*.vcf.gz* /gbdb/hg38/problematic/highRepro/
 
 # turns the beds into one single bed with the overlapped regions:
 for f in $(ls *.bed); do echo $f; n=${f/.bed/}; tawk -v name=${n} '{print $0,name}' $f > ${n}.bed4; done
 cat *.bed4 | sort -k1,1 -k2,2n > highRepro.allRegions
-bedOverlapMerge highRepro.allRegions > highRepro.merged
-bedToBigBed -type=bed3+ -tab -as=highRepro.as highRepro.merged ../../../chrom.sizes highRepro.bb
+bedOverlapMerge highRepro.allRegions | tawk '{print $0,0,".",$2,$2,"0,0,0",gensub(/\//, ",", "g",$4)}' > highRepro.merged
+bedToBigBed -type=bed9+1 -tab -as=highRepro.as highRepro.merged ../../../chrom.sizes highRepro.bb