7edc888861d9fd7769d0a21ae55d5f3e75e61587
markd
  Fri Aug 19 17:06:17 2016 -0700
Added genePredToProt that translates genePred files to protein.
It handles cases where there the annotations has frameshifting
indels described in the exonFrames column.  Partial codons will be skipped.
This differs from getRnaPred, which only handles initial, incomplete codons.

diff --git src/hg/utils/makefile src/hg/utils/makefile
index 706fb76..2c9b192 100644
--- src/hg/utils/makefile
+++ src/hg/utils/makefile
@@ -18,30 +18,31 @@
 endif
 
 # List of directories to build for userApps
 UTILS_APPLIST = \
 	bedExtendRanges \
 	bedToPsl \
 	bedWeedOverlapping \
 	bigPslToPsl \
 	chromGraphFromBin \
 	chromGraphToBin \
 	crTreeIndexBed \
 	crTreeSearchBed \
 	gapToLift \
 	genePredFilter \
 	genePredToBigGenePred \
+	genePredToProt \
 	gff3ToGenePred \
 	gff3ToPsl \
 	gtfToGenePred \
 	hubCheck \
 	hubPublicCheck \
 	makeTableList \
 	oligoMatch \
 	overlapSelect \
 	positionalTblCheck \
 	pslToBigPsl \
 	pslMap \
 	tdbQuery \
 	transMapPslToGenePred \
 	twoBitMask
 
@@ -54,30 +55,31 @@
 # List of directories to build of interest only at UCSC
 DIRS = ${buildRefresh} \
 	automation \
 	checkUrlsInTable \
 	geoMirrorNode \
 	makeTrackIndex \
 	mysqlSecurityCheck \
 	pslUniq \
 	refSeqGet \
 	safePush \
 	toDev64 \
 	wigBedToStep
 
 TEST_DIRS = \
 	genePredFilter \
+	genePredToProt \
 	gff3ToGenePred \
 	gff3ToPsl \
 	gtfToGenePred \
 	overlapSelect \
 	pslMap \
 	pslToBigPsl \
 	refSeqGet \
 	transMapPslToGenePred
 
 APPS = $(DIRS) $(UTILS_APPLIST)
 
 all:: utils
 
 utils: $(APPS:%=%.utils)
 %.utils: