New upstream version 1.0.0~rc2+dfsg

[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

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:

#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 \

			  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 \

			  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

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"

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

	$(MAKE) bin/$@

$(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)

#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

#### 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

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: