cf24bf1f4d870e1b6d2d9067c04ff480cfb469b2
lrnassar
  Fri Oct 20 12:54:49 2023 -0700
Adding an updated cosmic makedoc after a user wrote in with multiple errors found, refs #32430

diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt
index e0ef920..7c66c23 100644
--- src/hg/makeDb/doc/hg38/hg38.txt
+++ src/hg/makeDb/doc/hg38/hg38.txt
@@ -7041,30 +7041,32 @@
 
 #subtract to conform to bed format for all the items that have same star and endPos
 
 cat cosmic.fixed.bed | awk 'BEGIN {OFS="\t"} {
 if ($2 == $3)
         print $1,$2-1,$3,$4,$5,$6,$7,$8,$9;
 else
         print $0;
 }' > cosmic.fixedPos.bed
 
 bedToBigBed -type=bed6+3 -as=/hive/data/outside/cosmic/hg38/v98/cosmic.as /hive/data/outside/cosmic/hg38/v98/cosmic.fixedPos.bed /hive/data/genomes/hg38/chrom.sizes /hive/data/outside/cosmic/hg38/v98/cosmic.bb -tab
 
 #make symlink
 ln -s /hive/data/outside/cosmic/hg38/v98/cosmic.bb /gbdb/hg38/cosmic/cosmic.bb
 
+#This data has since been updated, see new makedoc doc/hg38/cosmicV98.txt and rm #32430
+
 ##############################################################################
 # LIFTOVER TO GCA_018873775.2_hg01243.v3.0 (DONE - 2023-08-13 - Hiram)
     ssh hgwdev
     # going to need an ooc for hg38.p14.2bit
     cd /hive/data/genomes/hg38
     time blat hg38.p14.2bit /dev/null /dev/null -tileSize=11 \
       -makeOoc=hg38.p14.ooc -repMatch=1024
     # Wrote 36808 overused 11-mers to hg38.p14.ooc
     # real    0m50.753s
 
     # and ooc for this GenArk hub
     cd /hive/data/genomes/asmHubs/genbankBuild/GCA/018/873/775/GCA_018873775.2_hg01243.v3.0
   time blat GCA_018873775.2_hg01243.v3.0.2bit /dev/null /dev/null -tileSize=11 \
       -makeOoc=GCA_018873775.2_hg01243.v3.0.ooc -repMatch=1024
 # Wrote 39087 overused 11-mers to GCA_018873775.2_hg01243.v3.0.ooc