05f7054ad0056072231e8bb4891287c54ed629e3
chmalee
  Tue Apr 13 11:10:01 2021 -0700
Fixing the gnomad structural variants deletion and duplication colors which were swapped both in the bigBed and the track description, refs #27363

diff --git src/hg/makeDb/gnomad/gnomadSvToUcsc.awk src/hg/makeDb/gnomad/gnomadSvToUcsc.awk
index 2b6bf0a..6ab6a72 100755
--- src/hg/makeDb/gnomad/gnomadSvToUcsc.awk
+++ src/hg/makeDb/gnomad/gnomadSvToUcsc.awk
@@ -1,114 +1,114 @@
 #!/usr/bin/awk -f
 # turn a gnomad SV file to ucsc bigBed 9+
 
 BEGIN {
     FS="\t";
     OFS="\t";
 }
 
 {
 chrom=$1
 start=$2
 end=$3
 origName=$4
 
 # get the list of genes affected for the mouseOver
 geneListStr=""
 numGenes = 0
 for (i = 5; i <= 12; i++)
     {
     if ($i != "NA" && $i != "True" && $i != "False")
         {
         newGeneCount = split($i,geneList,",");
         if (numGenes + newGeneCount <= 2)
             {
             for (j = 1; j <= newGeneCount; j++)
                 {
                 if (numGenes == 0 && j == 1) {geneListStr = geneList[j]}
                 else {geneListStr = geneListStr ", " geneList[j]}
                 }
             }
         else {geneListStr = "Too many genes affected, click on item for full list."}
         numGenes += newGeneCount;
         }
     }
 if (numGenes == 0) {geneListStr = "NA"}
 
 # make the list of affected genes for each type print nicely by adding a space after the commas
 for (i = 5; i <= 15; i++)
     gsub(",", ", ", $i)
 PROTEIN_CODING__COPY_GAIN=$5
 PROTEIN_CODING__DUP_LOF=$6
 PROTEIN_CODING__DUP_PARTIAL=$7
 PROTEIN_CODING__INTERGENIC=$8
 PROTEIN_CODING__INTRONIC=$9
 PROTEIN_CODING__INV_SPAN=$10
 PROTEIN_CODING__LOF=$11
 PROTEIN_CODING__MSV_EXON_OVR=$12
 PROTEIN_CODING__NEAREST_TSS=$13
 PROTEIN_CODING__PROMOTER=$14
 PROTEIN_CODING__UTR=$15
 
 # size of NA when variant is a breakend or something else
 if ($16 > 0)
     svlen=$16
 else
     svlen = "NA"
 svtype=$17
 an=$18
 ac=""
 af=""
 nhet=$21
 nhomalt=$22
 
 split($19,acArray,",")
 for (i = 1; i < length(acArray) - 1; i++)
     {
     ac = ac "" acArray[i] ", "
     }
 ac = ac "" acArray[length(acArray)]
 
 split($20,afArray,",")
 for (i = 1; i < length(afArray) - 1; i++)
     {
     af = af "" sprintf("%0.2g, ", afArray[i])
     }
 af = af "" sprintf("%0.2g", afArray[length(afArray)])
 
 split($4,a,"_")
 name=a[3] "_" a[4] "_" a[5]
 mouseOver = "Gene(s) affected: " geneListStr ", Position: " chrom ":" start+1 "-" end ", Size: " svlen ", Class: " svtype ", Allele Count: " ac ", Allele Number: " an ", Allele Frequency: " af
 
 color=""
 switch(svtype) {
     case "BND":
         color = "128,128,128"
         break
     case "CPX":
         color = "0,179,179"
         break
     case "CTX":
         color = "0,179,179"
         break
     case "DEL":
-        color = "0,0,255"
+        color = "255,0,0"
         break
     case "DUP":
-        color = "255,0,0"
+        color = "0,0,255"
         break
     case "INS":
         color = "255,165,0"
         break
     case "INV":
         color = "192,0,192"
         break
     case "MCNV":
         color = "0,179,179"
         break
     default:
         color = "154,182,160"
         break
 }
 
 print chrom, start, end, name, 0, ".", start, end, color, svlen, svtype, ac, an, af, nhet, nhomalt, PROTEIN_CODING__COPY_GAIN, PROTEIN_CODING__DUP_LOF, PROTEIN_CODING__DUP_PARTIAL, PROTEIN_CODING__INTERGENIC, PROTEIN_CODING__INTRONIC, PROTEIN_CODING__INV_SPAN, PROTEIN_CODING__LOF, PROTEIN_CODING__MSV_EXON_OVR, PROTEIN_CODING__NEAREST_TSS, PROTEIN_CODING__PROMOTER, PROTEIN_CODING__UTR, mouseOver
 }