Updated subrepos to lastest versions

mfumagalli · Feb 27, 2017 · 2f2e54e · 2f2e54e
1 parent 746455e
commit 2f2e54e
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Showing 8 changed files with 10 additions and 8 deletions.
diff --git a/Makefile b/Makefile
@@ -1,13 +1,14 @@
 
+export HTSSRC=../htslib/
+
 EXT = htslib angsd
 TOOLS = ngsSim ngsPopGen ngsUtils ngsDist ngsF ngsF-HMM
 
-
 all: $(EXT) $(TOOLS)
 
 .PHONY: $(EXT) $(TOOLS)
 $(EXT) $(TOOLS):
-	@$(MAKE) -C $@ HTSSRC=../htslib/;
+	@$(MAKE) -C $@
 
 test:
 	@for i in $(TOOLS); do $(MAKE) -C $$i test; done

diff --git a/README.md b/README.md
@@ -36,6 +36,7 @@ NOTE - this repository is intended for general use as it groups together the lat
 
 `ngsTools` can be easily installed but some packages have some external dependencies:
 
+* `gcc` : v4.9.2 tested on Debian 7.8 (wheezy)
 * `zlib`: v1.2.7 tested on Debian 7.8 (wheezy)
 * `gsl` : v1.15 tested on Debian 7.8 (wheezy)
 * `md5sum`: only needed for `make test`

diff --git a/ngsDist b/ngsDist
diff --git a/ngsF b/ngsF
diff --git a/ngsF-HMM b/ngsF-HMM
diff --git a/ngsPopGen b/ngsPopGen
diff --git a/ngsSim b/ngsSim
diff --git a/ngsUtils b/ngsUtils
+3 −6		.gitignore
+4 −3		Makefile
+1 −1		examples/test.sh
+3 −17		ngsDist.cpp
+1 −0		ngsDist.hpp
+10 −2		parse_args.cpp
+236 −0		shared/HMM.cpp
+15 −0		shared/HMM.hpp
+5 −0		shared/bfgs.h
+91 −43		shared/gen_func.cpp
+16 −10		shared/gen_func.hpp
+25 −16		shared/read_data.cpp
+1 −1		shared/read_data.hpp
+18 −8		Makefile
+2 −7		examples/README.md
+0 −1		examples/test.md5
+2 −7		examples/test.sh
+1 −1		htslib/Makefile
+0 −0		htslib/bgzf.c
+0 −0		htslib/bgzf.h
+0 −0		htslib/bgzip.c
+0 −0		htslib/khash.h
+0 −0		htslib/knetfile.c
+0 −0		htslib/knetfile.h
+13 −1		ngsF.sh
+1 −1		shared.h
+4 −0		.gitignore
+102 −14		EM.cpp
+0 −276		HMM.cpp
+0 −13		HMM.hpp
+5 −5		Makefile
+1 −0		README.md
+2 −7		examples/README.md
+1 −1		examples/test.md5
+2 −4		examples/test.sh
+10 −6		ngsF-HMM.cpp
+14 −4		ngsF-HMM.sh
+3 −1		parse_args.cpp
+236 −0		shared/HMM.cpp
+15 −0		shared/HMM.hpp
+5 −0		shared/bfgs.h
+85 −45		shared/gen_func.cpp
+16 −10		shared/gen_func.hpp
+25 −16		shared/read_data.cpp
+1 −1		shared/read_data.hpp