.gitmodules

@@ -19,3 +19,9 @@
 [submodule "filevercmp"]
 	path = filevercmp
 	url = https://github.com/ekg/filevercmp.git
+[submodule "googletest"]
+	path = googletest
+	url = https://github.com/google/googletest.git
+[submodule "libVCFH"]
+	path = libVCFH
+	url = https://github.com/edawson/libVCFH.git

.travis.yml

@@ -3,7 +3,12 @@ sudo: required
 compiler: 
     - gcc
 before_install:
- - sudo apt-get install g++
+    - sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
+    - ls /etc/apt/sources.list.d
+    - sudo apt-get update
+    - sudo apt-get install -qq gcc-4.9 g++-4.9
+    - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9
+    - gcc --version && g++ --version
     - sudo apt-get install build-essential
     - git submodule update --init --recursive
 os:

Makefile

@@ -25,8 +25,10 @@ OBJ_DIR:=obj
 #vcfstats.cpp
 
 BIN_SOURCES = src/vcfecho.cpp \
+			  src/vcfnormalizesvs.cpp \
 			  src/dumpContigsFromHeader.cpp \
 			  src/bFst.cpp \
+			  src/pVst.cpp \
 			  src/hapLrt.cpp \
 			  src/popStats.cpp \
 			  src/wcFst.cpp \
@@ -37,7 +39,7 @@ BIN_SOURCES = src/vcfecho.cpp \
 			  src/sequenceDiversity.cpp \
 			  src/pFst.cpp \
 			  src/smoother.cpp \
-			  src/LD.cpp \
+			  src/vcfld.cpp \
 			  src/plotHaps.cpp \
 			  src/abba-baba.cpp \
 			  src/permuteGPAT++.cpp \
@@ -105,6 +107,8 @@ BIN_SOURCES = src/vcfecho.cpp \
 			  src/vcfqual2info.cpp \
 			  src/vcfinfo2qual.cpp \
 			  src/vcfglbound.cpp \
+			  src/vcfunphase.cpp \
+			  src/vcfnull2ref.cpp \
 			  src/vcfinfosummarize.cpp
 
 # when we can figure out how to build on mac
@@ -125,23 +129,24 @@ FSOM = fsom/fsom.o
 FILEVERCMP = filevercmp/filevercmp.o
 
 INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp
+LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2
 
 
-all: $(OBJECTS) $(BINS)
+all: $(OBJECTS) $(BINS) scriptToBin
 
+scriptToBin: $(BINS)
+	cp scripts/* bin
 
 GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
 
-CXX = g++
-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"$(GIT_VERSION)\"
+CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x
 #CXXFLAGS = -O2
 #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
 
 SSW = src/ssw.o src/ssw_cpp.o
 
-ssw.o: src/ssw.h
-ssw_cpp.o:src/ssw_cpp.h
+ssw.o: src/ssw.hpp
+ssw_cpp.o:src/ssw_cpp.hpp
 
 openmp:
 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
@@ -152,7 +157,7 @@ profiling:
 gprof:
 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
 
-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
+$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
 	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
 
 multichoose: pre
@@ -188,7 +193,7 @@ $(SHORTBINS): pre
 	$(MAKE) bin/$@
 
 $(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
-	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
+	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
 
 libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
 	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)

Makefile.old

-#OBJ_DIR = ./
-HEADERS = src/Variant.h \
-		  src/split.h \
-		  src/join.h
-SOURCES = src/Variant.cpp \
-		  src/split.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-
-# TODO
-#vcfstats.cpp
-
-BIN_SOURCES = src/vcfecho.cpp \
-			  src/vcfaltcount.cpp \
-			  src/vcfhetcount.cpp \
-			  src/vcfhethomratio.cpp \
-			  src/vcffilter.cpp \
-			  src/vcf2tsv.cpp \
-			  src/vcfgenotypes.cpp \
-			  src/vcfannotategenotypes.cpp \
-			  src/vcfcommonsamples.cpp \
-			  src/vcfremovesamples.cpp \
-			  src/vcfkeepsamples.cpp \
-			  src/vcfsamplenames.cpp \
-			  src/vcfgenotypecompare.cpp \
-			  src/vcffixup.cpp \
-			  src/vcfclassify.cpp \
-			  src/vcfsamplediff.cpp \
-			  src/vcfremoveaberrantgenotypes.cpp \
-			  src/vcfrandom.cpp \
-			  src/vcfparsealts.cpp \
-			  src/vcfstats.cpp \
-			  src/vcfflatten.cpp \
-			  src/vcfprimers.cpp \
-			  src/vcfnumalt.cpp \
-			  src/vcfcleancomplex.cpp \
-			  src/vcfintersect.cpp \
-			  src/vcfannotate.cpp \
-			  src/vcfallelicprimitives.cpp \
-			  src/vcfoverlay.cpp \
-			  src/vcfaddinfo.cpp \
-			  src/vcfkeepinfo.cpp \
-			  src/vcfkeepgeno.cpp \
-			  src/vcfafpath.cpp \
-			  src/vcfcountalleles.cpp \
-			  src/vcflength.cpp \
-			  src/vcfdistance.cpp \
-			  src/vcfrandomsample.cpp \
-			  src/vcfentropy.cpp \
-			  src/vcfglxgt.cpp \
-			  src/vcfroc.cpp \
-			  src/vcfcheck.cpp \
-			  src/vcfstreamsort.cpp \
-			  src/vcfuniq.cpp \
-			  src/vcfuniqalleles.cpp \
-			  src/vcfremap.cpp \
-			  src/vcf2fasta.cpp \
-			  src/vcfsitesummarize.cpp \
-			  src/vcfbreakmulti.cpp \
-			  src/vcfcreatemulti.cpp \
-			  src/vcfevenregions.cpp \
-			  src/vcfcat.cpp \
-			  src/vcfgenosummarize.cpp \
-			  src/vcfgenosamplenames.cpp \
-			  src/vcfgeno2haplo.cpp \
-			  src/vcfleftalign.cpp \
-			  src/vcfcombine.cpp \
-			  src/vcfgeno2alleles.cpp \
-			  src/vcfindex.cpp \
-			  src/vcf2dag.cpp \
-			  src/vcfsample2info.cpp \
-			  src/vcfqual2info.cpp \
-			  src/vcfinfo2qual.cpp \
-			  src/vcfglbound.cpp \
-			  src/vcfinfosummarize.cpp
-
-# when we can figure out how to build on mac
-# src/vcfsom.cpp
-
-#BINS = $(BIN_SOURCES:.cpp=)
-BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
-SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
-
-TABIX = tabixpp/tabix.o
-FASTAHACK = fastahack/Fasta.o
-SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o 
-REPEATS = smithwaterman/Repeats.o
-INDELALLELE = smithwaterman/IndelAllele.o
-DISORDER = smithwaterman/disorder.o
-LEFTALIGN = smithwaterman/LeftAlign.o
-FSOM = fsom/fsom.o
-FILEVERCMP = filevercmp/filevercmp.o
-
-INCLUDES = -I. -Itabixpp/htslib/ -L. -Ltabixpp/ -Ltabixpp/htslib/
-LDFLAGS = -lvcflib -lhts -lpthread -lz -lm
-
-
-all: $(OBJECTS) $(BINS)
-
-CXX = g++
-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64
-#CXXFLAGS = -O2
-#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
-
-SSW = src/ssw.o src/ssw_cpp.o
-
-ssw.o: src/ssw.h
-ssw_cpp.o:src/ssw_cpp.h
-
-openmp:
-	$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
-
-profiling:
-	$(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all
-
-gprof:
-	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
-
-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX)
-	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
-
-$(TABIX):
-	cd tabixpp && $(MAKE)
-
-$(SMITHWATERMAN):
-	cd smithwaterman && $(MAKE)
-
-$(DISORDER): $(SMITHWATERMAN)
-
-$(REPEATS): $(SMITHWATERMAN)
-
-$(LEFTALIGN): $(SMITHWATERMAN)
-
-$(INDELALLELE): $(SMITHWATERMAN)
-
-$(FASTAHACK):
-	cd fastahack && $(MAKE)
-
-#$(FSOM):
-#	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
-
-$(FILEVERCMP):
-	cd filevercmp && make
-
-$(SHORTBINS):
-	$(MAKE) bin/$@
-
-$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP)
-	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
-
-libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX)
-	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
-
-
-test: $(BINS)
-	@prove -Itests/lib -w tests/*.t
-
-clean:
-	rm -f $(BINS) $(OBJECTS)
-	rm -f ssw_cpp.o ssw.o
-	rm -f libvcflib.a
-	cd tabixpp && make clean
-	cd smithwaterman && make clean
-	cd fastahack && make clean
-
-.PHONY: clean all test

README.md

@@ -5,7 +5,7 @@
 
 #### license: MIT
 
-[![Gitter](https://badges.gitter.im/Join Chat.svg)](https://gitter.im/ekg/vcflib?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![Build Status](https://travis-ci.org/vcflib/vcflib.svg?branch=master)](https://travis-ci.org/vcflib/vcflib)
+[![Gitter](https://badges.gitter.im/ekg/vcflib.svg)](https://gitter.im/ekg/vcflib?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![Build Status](https://travis-ci.org/vcflib/vcflib.svg?branch=master)](https://travis-ci.org/vcflib/vcflib)
 ---
 
 ## overview
@@ -25,6 +25,19 @@ It is both:
 The API itself provides a quick and extremely permissive method to read and write VCF files.
 Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.
 
+## download and install 
+
+1. Under the repository name, click to copy the clone URL for the repository. ![](https://help.github.com/assets/images/help/repository/clone-repo-clone-url-button.png)
+
+2. Go to the location where you want the cloned directory to be made:  `cd <PathWhereIWantToCloneVcflib>`
+
+3. Type `git clone --recursive`, and then paste the URL you copied in Step 1.
+
+4. Enter the cloned directory and type `make` to compile the programs.  If you want to use threading type `make openmp` instead of `make`.  Only a few VCFLIB tools are threaded.
+
+5. Once make is finished the executables are ready in the folder `<PathWhereIWantToCloneVcflib>/vcflib/bin/`. Set this path as an  environment variable in the .bashrc file to access executables form everywhere on your proile OR call the executables from the path where they are. 
+
+
 ## usage
 
 vcflib provides a variety of functions for VCF manipulation:

debian/changelog

-libvcflib (1.0.0~rc1+dfsg1-7) UNRELEASED; urgency=medium
+libvcflib (1.0.0~rc2+dfsg-1) UNRELEASED; urgency=medium
 
+  [ Steffen Moeller ]
   * Created debian/upstream/metadata for references to
     registries.
 
- -- Steffen Moeller <moeller@debian.org>  Mon, 30 Oct 2017 16:12:34 +0100
+  [ Andreas Tille ]
+  * New upstream version
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Versioned Build-Depends: libfastahack-dev (>= 0.0+git20160702.bbc645f+dfsg-5~)
+  * Fix header file name
+  * Build-Depends: libbz2-dev
+  * Fix installation target dir
+
+ -- Andreas Tille <tille@debian.org>  Thu, 13 Sep 2018 16:06:09 +0200
 
 libvcflib (1.0.0~rc1+dfsg1-6) unstable; urgency=medium
 

debian/compat

-10
+11

debian/control

@@ -3,19 +3,20 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                dh-exec,
                python-markdown,
                libtabixpp-dev,
+               libbz2-dev,
                libdisorder-dev,
                libsmithwaterman-dev (>= 0.0+20160702-2),
                libssw-dev,
-               libfastahack-dev,
+               libfastahack-dev (>= 0.0+git20160702.bbc645f+dfsg-5~),
                pkg-config,
                libipc-run3-perl
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libvcflib.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/libvcflib.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/libvcflib
+Vcs-Git: https://salsa.debian.org/med-team/libvcflib.git
 Homepage: https://github.com/ekg/vcflib
 
 Package: libvcflib1

debian/libvcflib-tools.install

-bin/*.R			usr/lib/R/site-library/vcflib
+binaries/*.R		usr/lib/R/site-library/vcflib
 binaries		usr/lib/vcflib
 debian/wrapper/*	usr/bin

debian/patches/filevercmp.h.patch

@@ -12,7 +12,7 @@ Description: Inject two files via quilt patch
 
 --- a/Makefile
 +++ b/Makefile
-@@ -186,7 +186,12 @@
+@@ -191,7 +191,12 @@ $(FASTAHACK): pre
  #	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
  
  $(FILEVERCMP): pre

debian/patches/fix_installation.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 13 Sep 2018 19:35:33 +0200
+Description: Upstream should use consistent installation target dir
+
+--- a/Makefile
++++ b/Makefile
+@@ -133,7 +133,7 @@ LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -l
+ all: $(OBJECTS) $(BINS) scriptToBin
+ 
+ scriptToBin: $(BINS)
+-	cp scripts/* bin
++	cp scripts/* $(BIN_DIR)
+ 
+ GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
+ 

debian/patches/fix_ssw_cpp_header_name.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 13 Sep 2018 19:35:33 +0200
+Description: The header file is named ssw_cpp.h
+
+--- a/src/Variant.h
++++ b/src/Variant.h
+@@ -20,7 +20,7 @@
+ #include "tabix.hpp"
+ #include "SmithWatermanGotoh.h"
+ #include "disorder.h"
+-#include "ssw_cpp.hpp"
++#include <ssw_cpp.h>
+ #include "convert.h"
+ #include "multichoose.h"
+ #include "Fasta.h"

debian/patches/intervaltree.patch

@@ -5,7 +5,7 @@ Description: We provide a local copy of intervaltree in debian/include and
 
 --- a/Makefile
 +++ b/Makefile
-@@ -160,6 +160,7 @@ multichoose: pre
+@@ -166,6 +166,7 @@ multichoose: pre
  intervaltree: pre
  	echo "Source does not contain dir intervaltree"
  	# cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/

debian/patches/keep_R_files.patch

@@ -15,7 +15,7 @@ Description: There is a dir bin/ containing some R files which
  LIB_DIR:=lib
  SRC_DIR=src
  INC_DIR:=include
-@@ -111,7 +111,7 @@ BIN_SOURCES = src/vcfecho.cpp \
+@@ -115,7 +115,7 @@ BIN_SOURCES = src/vcfecho.cpp \
  # src/vcfsom.cpp
  
  #BINS = $(BIN_SOURCES:.cpp=)
@@ -24,7 +24,7 @@ Description: There is a dir bin/ containing some R files which
  SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
  
  # TABIX = tabixpp/tabix.o
-@@ -177,7 +177,7 @@ $(FILEVERCMP): pre
+@@ -183,7 +183,7 @@ $(FILEVERCMP): pre
  	ln -sf ../filevercmp/filevercmp.h $(VCF_LIB_LOCAL)/$(INC_DIR)/filevercmp.h
  
  $(SHORTBINS): pre
@@ -32,4 +32,4 @@ Description: There is a dir bin/ containing some R files which
 +	$(MAKE) $(BIN_DIR)/$@
  
  $(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
- 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
+ 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"

debian/patches/series

@@ -8,3 +8,5 @@ shared_lib.patch
 keep_R_files.patch
 use_debian_packaged_libssw.patch
 pkg-config.patch
+fix_ssw_cpp_header_name.patch
+fix_installation.patch

debian/patches/shared_lib.patch

@@ -4,7 +4,7 @@ Description: Create shared lib instead of static
 
 --- a/Makefile
 +++ b/Makefile
-@@ -115,11 +115,11 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
+@@ -119,11 +119,11 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
  SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
  
  # TABIX = tabixpp/tabix.o
@@ -21,12 +21,12 @@ Description: Create shared lib instead of static
  FSOM = fsom/fsom.o
  FILEVERCMP = filevercmp/filevercmp.o
  
-@@ -138,8 +138,11 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
+@@ -143,8 +143,11 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
  
  SSW = src/ssw.o src/ssw_cpp.o
  
--ssw.o: src/ssw.h
--ssw_cpp.o:src/ssw_cpp.h
+-ssw.o: src/ssw.hpp
+-ssw_cpp.o:src/ssw_cpp.hpp
 +src/ssw.o: src/ssw.h src/ssw.c
 +	$(CXX) -c $(CFLAGS) -fPIC -o $@ src/$(*F).c
 +
@@ -35,16 +35,16 @@ Description: Create shared lib instead of static
  
  openmp:
  	$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
-@@ -151,7 +154,7 @@ gprof:
- 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
+@@ -157,7 +160,7 @@ gprof:
  
+ $(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
  $(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
 -	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
 +	$(CXX) -c $(CFLAGS) -fPIC -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  
  multichoose: pre
  	echo "Source does not contain dir multichoose"
-@@ -162,22 +165,6 @@ intervaltree: pre
+@@ -168,22 +171,6 @@ intervaltree: pre
  	# cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  	mkdir -p $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp -a debian/include/* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  
@@ -67,7 +67,7 @@ Description: Create shared lib instead of static
  #$(FSOM):
  #	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
  
-@@ -186,19 +173,20 @@ $(FILEVERCMP): pre
+@@ -192,18 +179,20 @@ $(FILEVERCMP): pre
  	#cp /usr/share/gnulib/lib/filevercmp.* filevercmp
  	#echo 'Proper use of filevercmp would be: `gnulib-tool --import filevercmp` - but it needs ./configure.ac'
  	#We here go with quilt patches from upstream files
@@ -80,21 +80,20 @@ Description: Create shared lib instead of static
  
 -$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
 +$(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
- 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
+ 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
  
 -libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
 -	ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
 -	cp libvcflib.a $(LIB_DIR)
--
 +libvcflib.so: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
 +	# ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
 +	gcc -shared  -Wl,-soname -Wl,libvcflib.so.1 -o libvcflib.so.1 $(OBJECTS) $(SSW) $(FILEVERCMP)
 +	ln -s libvcflib.so.1 libvcflib.so
 +	cp -a libvcflib.so* $(LIB_DIR)
  
+ 
  test: $(BINS)
- 	@prove -Itests/lib -w tests/*.t
-@@ -218,7 +206,7 @@ update: pull all
+@@ -224,7 +213,7 @@ update: pull all
  clean:
  	rm -f $(BINS) $(OBJECTS)
  	rm -f ssw_cpp.o ssw.o

debian/patches/use_debian_packaged_fastahack.patch

@@ -4,27 +4,37 @@ Description: Use Debian packaged libfastahack (and libdisorder)
 
 --- a/Makefile
 +++ b/Makefile
-@@ -115,7 +115,6 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
+@@ -119,7 +119,6 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
  SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
  
  # TABIX = tabixpp/tabix.o
--FASTAHACK = fastahack/Fasta.o
+-# FASTAHACK = fastahack/Fasta.o
  SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
  REPEATS = smithwaterman/Repeats.o
  INDELALLELE = smithwaterman/IndelAllele.o
-@@ -124,9 +123,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
+@@ -128,8 +127,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
  FSOM = fsom/fsom.o
  FILEVERCMP = filevercmp/filevercmp.o
  
 -INCLUDES = `pkg-config --cflags libsmithwaterman` -I$(INC_DIR)
--LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman`
--
+-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp `pkg-config --libs libsmithwaterman`
 +INCLUDES = `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -I$(INC_DIR)
-+LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder
++LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder
+ 
+ all: $(OBJECTS) $(BINS) scriptToBin
+ 
+@@ -156,8 +155,8 @@ profiling:
+ gprof:
+ 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
  
- all: $(OBJECTS) $(BINS)
+-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
+-$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
++$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
++$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
+ 	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  
-@@ -179,9 +177,6 @@ $(LEFTALIGN): $(SMITHWATERMAN)
+ multichoose: pre
+@@ -184,9 +183,6 @@ $(LEFTALIGN): $(SMITHWATERMAN)
  
  $(INDELALLELE): $(SMITHWATERMAN)
  
@@ -34,13 +44,13 @@ Description: Use Debian packaged libfastahack (and libdisorder)
  #$(FSOM):
  #	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
  
-@@ -196,11 +191,11 @@ $(FILEVERCMP): pre
+@@ -201,11 +197,11 @@ $(FILEVERCMP): pre
  $(SHORTBINS): pre
  	$(MAKE) bin/$@
  
 -$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
 +$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
- 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
+ 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
  
 -libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
 -	ar rs libvcflib.a $(OBJECTS) $(FASTAHACK) $(SSW) $(FILEVERCMP)
@@ -49,7 +59,7 @@ Description: Use Debian packaged libfastahack (and libdisorder)
  	cp libvcflib.a $(LIB_DIR)
  
  
-@@ -229,6 +224,6 @@ clean:
+@@ -234,6 +230,6 @@ clean:
  	rm -rf $(OBJ_DIR)
  	# cd tabixpp && make clean
  	# cd smithwaterman && make clean

debian/patches/use_debian_packaged_libssw.patch

@@ -6,7 +6,7 @@ Description: Use Debian packaged libssw (while its not clear
 
 --- a/Makefile
 +++ b/Makefile
-@@ -136,13 +136,7 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
+@@ -141,13 +141,7 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
  #CXXFLAGS = -O2
  #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
  

debian/patches/use_debian_packaged_smithwaterman.patch

@@ -4,18 +4,18 @@ Description: Use Debian packaged libsmithwaterman
 
 --- a/Makefile
 +++ b/Makefile
-@@ -124,8 +124,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
+@@ -128,8 +128,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
  FSOM = fsom/fsom.o
  FILEVERCMP = filevercmp/filevercmp.o
  
 -INCLUDES = -I$(INC_DIR)
--LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp
+-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp
 +INCLUDES = `pkg-config --cflags libsmithwaterman` -I$(INC_DIR)
-+LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman`
++LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp `pkg-config --libs libsmithwaterman`
  
+ all: $(OBJECTS) $(BINS) scriptToBin
  
- all: $(OBJECTS) $(BINS)
-@@ -156,17 +156,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) multic
+@@ -161,17 +161,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) multic
  	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  
  multichoose: pre
@@ -39,8 +39,8 @@ Description: Use Debian packaged libsmithwaterman
  
  $(DISORDER): $(SMITHWATERMAN)
  
-@@ -192,7 +195,7 @@ $(BINS): $(BIN_SOURCES) libvcflib.a $(OB
- 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
+@@ -197,7 +200,7 @@ $(BINS): $(BIN_SOURCES) libvcflib.a $(OB
+ 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
  
  libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
 -	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP)
@@ -48,7 +48,7 @@ Description: Use Debian packaged libsmithwaterman
  	cp libvcflib.a $(LIB_DIR)
  
  
-@@ -220,7 +223,7 @@ clean:
+@@ -225,7 +228,7 @@ clean:
  	rm -rf $(INC_DIR)
  	rm -rf $(OBJ_DIR)
  	# cd tabixpp && make clean

debian/patches/use_debian_packaged_tabixpp.patch

@@ -4,36 +4,38 @@ Description: Use Debian packaged libtabixpp
 
 --- a/Makefile
 +++ b/Makefile
-@@ -114,7 +114,7 @@ BIN_SOURCES = src/vcfecho.cpp \
+@@ -118,8 +118,8 @@ BIN_SOURCES = src/vcfecho.cpp \
  BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
  SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
  
 -TABIX = tabixpp/tabix.o
+-FASTAHACK = fastahack/Fasta.o
 +# TABIX = tabixpp/tabix.o
- FASTAHACK = fastahack/Fasta.o
++# FASTAHACK = fastahack/Fasta.o
  SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
  REPEATS = smithwaterman/Repeats.o
-@@ -124,8 +124,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
+ INDELALLELE = smithwaterman/IndelAllele.o
+@@ -128,9 +128,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
  FSOM = fsom/fsom.o
  FILEVERCMP = filevercmp/filevercmp.o
  
 -INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
--LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp
+-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2
+-
 +INCLUDES = -I$(INC_DIR)
-+LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp
++LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp
  
+ all: $(OBJECTS) $(BINS) scriptToBin
  
- all: $(OBJECTS) $(BINS)
-@@ -152,7 +152,7 @@ profiling:
- gprof:
+@@ -158,6 +157,7 @@ gprof:
  	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
  
--$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
-+$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
+ $(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
++$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
  	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  
  multichoose: pre
-@@ -162,7 +162,8 @@ intervaltree: pre
+@@ -167,7 +167,8 @@ intervaltree: pre
  	cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  
  $(TABIX): pre
@@ -43,9 +45,9 @@ Description: Use Debian packaged libtabixpp
  
  $(SMITHWATERMAN): pre
  	cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
-@@ -190,8 +191,8 @@ $(SHORTBINS): pre
+@@ -195,8 +196,8 @@ $(SHORTBINS): pre
  $(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
- 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
+ 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
  
 -libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
 -	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
@@ -54,7 +56,7 @@ Description: Use Debian packaged libtabixpp
  	cp libvcflib.a $(LIB_DIR)
  
  
-@@ -218,7 +219,7 @@ clean:
+@@ -223,7 +224,7 @@ clean:
  	rm -rf $(LIB_DIR)
  	rm -rf $(INC_DIR)
  	rm -rf $(OBJ_DIR)