11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/hg/pslCDnaGenomeMatch/makefile src/hg/pslCDnaGenomeMatch/makefile
index 7554c6d..f4c7a90 100644
--- src/hg/pslCDnaGenomeMatch/makefile
+++ src/hg/pslCDnaGenomeMatch/makefile
@@ -1,45 +1,46 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm $(MYSQLLIBS)
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a 
 
 M = pslCDnaGenomeMatch.o  
 DB=hg18
 
 O = pslMismatch.o misMatch.o 
 pslCDnaGenomeMatch: $M $(MYLIBS)
 	gcc -ggdb -o ${BINDIR}/pslCDnaGenomeMatch $M $(MARKDEBUG) $(MYLIBS) $L 
 #${STRIP} ${BINDIR}/pslCDnaGenomeMatch${EXE}
 
 misMatch: $O $(MYLIBS)
 	gcc -ggdb -o ${BINDIR}/misMatch  $O $(MARKDEBUG) $(MYLIBS) $L 
 
 lib:
 	cd ../../lib && ${MAKE}
 
 test: test14 test15 test16 mrna1 mrna5 mrna13b mrna13c rest1 testDA9 pass1733 mrnaDrop 
 t%:	input/t%.psl
 	${MKDIR} output
 	DB=hg18
 	pslCDnaGenomeMatch -verbose=4 -bedOut=output/$@.bed input/$@.psl /hive/users/baertsch/retro/${DB}/S1.len /hive/users/baertsch/retro/${DB}/est.2bit /hive/data/genomes/${DB}/nib output/$@.psl -score=output/$@.tab -minDiff=5  > $@.log 
 	diff expected/$@.psl output/$@.psl 
 	rm -f $@.log
 r%:	input/r%.psl
 	${MKDIR} output
 	pslCDnaGenomeMatch -verbose=4 -bedOut=output/$@.bed input/$@.psl /hive/users/baertsch/retro/mm9/S1.len /hive/users/baertsch/retro/mm9/est.2bit /hive/data/genomes/mm9/nib output/$@.psl -score=output/$@.tab -minDiff=3 -notAlignPenalty=3 > $@.log 
 	diff expected/$@.psl output/$@.psl 
 #rm -f $@.log
 m%:	input/m%.psl
 	${MKDIR} output
 	pslCDnaGenomeMatch -verbose=4 -bedOut=output/$@.bed input/$@.psl /hive/users/baertsch/retro/${DB}/S1.len /hive/data/genomes/${DB}/bed/mrnaBlastz/mrnaNoversion.2bit /hive/data/genomes/${DB}/nib output/$@.psl -score=output/$@.tab -notAlignPenalty=8 -minDiff=3  > $@.log 
 	diff expected/$@.psl output/$@.psl 
 #	diff expected/$@.tab output/$@.tab 
 	rm -f $@.log
 p%:	input/p%.psl
 	${MKDIR} output
 	pslCDnaGenomeMatch -verbose=4 -bedOut=output/$@.bed input/$@.psl /hive/users/baertsch/retro/${DB}/S1.len /hive/data/genomes/${DB}/bed/mrnaBlastz/mrnaNoversion.2bit /hive/data/genomes/${DB}/nib output/$@.psl -score=output/$@.tab -minDiff=5  -passthru > $@.log 
 	diff expected/$@.psl output/$@.psl 
 	rm -f $@.log
 clean:
 	rm -rf output