Bugfixes

[htsworkflow.git] / htswanalysis / src / GetReadsInSnps / Makefile

diff --git a/htswanalysis/src/GetReadsInSnps/Makefile b/htswanalysis/src/GetReadsInSnps/Makefile
index f8c348851cffc8beaaaf6b77a29c2ff9e8891ac0..ae11c5c8d9466efa7fc92367a82a2635c8a2295c 100644 (file)
--- a/htswanalysis/src/GetReadsInSnps/Makefile
+++ b/htswanalysis/src/GetReadsInSnps/Makefile
@@ -1,10 +1,16 @@
 CPPFLAGS=-g -Wall -I/opt/local/include
 #LDFLAGS=-lgsl -lgslcblas -lm -lduma -L/opt/local/lib
 #CPPFLAGS=-g -Wall -O3 -I/opt/local/include
-LDFLAGS=-lgsl -lgslcblas -lm -L/opt/local/lib
+LDFLAGS=-lgsl -lgslcblas -lm -L/opt/local/lib -L../SRLib
+
+all: getReadsInSnps
+
+getReadsInSnps: getReadsInSnps.o ../SRLib/Loci.o ../SRLib/Read.o ../SRLib/SNP.o ../SRLib/Util.o
+       g++ $(LDFLAGS) -L../SRLib $^ -o $@
 
 all: patch_genome getReadsInSnps getRegionConsensus
 
 patch_genome: patch_genome.cpp chrom_list.cpp util.cpp
 
-getRegionConsensus: getRegionConsensus.cpp chrom_list.cpp util.cpp
+getRegionConsensus: ../SRLib/chrom_list.o ../SRLib/util.o ../SRLib/read.o ../SRLib/loci.o ../SRLib/nuc.o
+       g++ getRegionConsensus.cpp $(CPPFLAGS) $(LDFLAGS) $^ -o $@