659e6be1bf5c1f6d61c656527a6e3888f6453c76
hiram
  Sun Oct 5 12:12:53 2014 -0700
adding mafToSnpBed to the utils build refs #14079
diff --git src/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
index 932b6eb..cf31584 100755
--- src/userApps/fetchKentSource.sh
+++ src/userApps/fetchKentSource.sh
@@ -20,30 +20,34 @@
 
 # the combined samtabix source for the SAM/BAM/TABIX functions:
 rm -fr samtabix
 echo "fetch samtabix" 1>&2
 git clone http://genome-source.cse.ucsc.edu/samtabix.git samtabix \
   > /dev/null 2>&1
 
 # These selective git archive commands only work up to a certain size
 # of fetched source (number of arguments), hence the multiple set of
 # individual fetches to get all the parts
 
 rm -f part1Src.zip part2Src.zip part3Src.zip part4Src.zip part5Src.zip
 export partNumber=1
 export ofN="of 5"
 
+# this util changed from being in a directory to being a script
+# the extract can't overwrite the directory with a file
+rm -fr kent/src/uniprotLift
+
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/machTest.sh \
 src/ameme \
 src/aladdin \
 src/blat \
 src/dnaDust \
 src/fuse \
 src/gfClient \
 src/gfServer \
 src/index \
 src/makefile \
 src/meta \
 src/parasol \
@@ -176,32 +180,30 @@
 src/hg/pslRecalcMatch \
 src/hg/pslSelect \
 src/hg/pslSimp \
 src/hg/pslSortAcc \
 src/hg/pslSplitOnTarget \
 src/hg/pslStats \
 src/hg/pslSwap \
 src/hg/pslToBed \
 src/hg/pslUnpile \
 src/hg/pslxToFa \
 src/hg/qa \
 src/hg/qaToQac \
 src/hg/qacAgpLift \
 src/hg/qacToQa \
 src/hg/qacToWig \
-src/hg/ratStuff/mafsInRegion \
-src/hg/ratStuff/mafSpeciesSubset \
 src/hg/recycleDb \
 src/hg/relPairs \
 src/hg/reviewSanity \
 src/hg/rnaStructure \
 src/hg/scanRa \
 src/hg/semiNorm \
 src/hg/sim4big \
 src/hg/snp \
 src/hg/snpException \
 src/hg/spideyToPsl \
 src/hg/encode3 \
 src/hg/splitFa \
 src/hg/splitFaIntoContigs \
 src/hg/sqlEnvTest.sh \
 src/hg/sqlToXml \