976e5f5a2582e99913f82839e86efccdca88d814
angie
  Fri Mar 22 13:12:51 2013 -0700
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts.  For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt.  Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152

diff --git src/hg/utils/makefile src/hg/utils/makefile
index c2c9218..ebe48ce 100644
--- src/hg/utils/makefile
+++ src/hg/utils/makefile
@@ -1,76 +1,78 @@
 # Build all directories in utils
 # test comment
 # 	$Id: makefile,v 1.21 2010/06/04 00:12:42 larrym Exp $
 
 include ../../inc/common.mk
 
 
 SCRIPT_FILES = \
+	dbNsfpToBed.pl \
 	dumpDb.pl \
-	mergeOverlapBed4.pl
+	mergeOverlapBed4.pl \
+	mergeSortedBed3Plus.pl
 
 # List of directories to build
 USE_DIRS = $(DIRS)
 
 DIRS = \
 	bedToPsl \
 	bedExtendRanges \
 	bedWeedOverlapping \
 	chromGraphFromBin \
 	chromGraphToBin \
 	crTreeIndexBed \
 	crTreeSearchBed \
 	gapToLift \
 	hubCheck hubPublicCheck \
         makeTableList \
 	oligoMatch \
 	positionalTblCheck \
 	safePush \
 	toDev64 \
 	twoBitMask \
 	gff3ToGenePred \
 	gff3ToPsl \
 	gtfToGenePred \
 	automation \
 	refreshNamedSessionCustomTracks \
 	refSeqGet \
 	tdbQuery \
 	wigBedToStep \
 	overlapSelect \
 	pslMap \
 	pslUniq \
 	makeTrackIndex \
 	geoMirrorNode
 
 TEST_DIRS = \
 	gff3ToGenePred \
 	gff3ToPsl \
 	gtfToGenePred \
 	overlapSelect \
 	pslMap \
 	refSeqGet
 
 
 all:: utils
 
 utils: $(USE_DIRS:%=%.utils)
 %.utils:
 	(cd $* && $(MAKE))
 
 scripts: $(SCRIPT_FILES:%=%.scripts)
 %.scripts:
 	chmod +x $*
 	rm -f ${SCRIPTS}/$*
 	cp -p $* ${SCRIPTS}/$*
 
 alpha: scripts all
 
 test::	${TEST_DIRS:%=%.test}
 %.test:
 	(cd $* && ${MAKE} test)
 
 clean:: $(USE_DIRS:%=%.clean)
 	- find . -name '*.o' -exec rm {} \;
 %.clean:
 	(cd $* && ${MAKE} clean)