[submodule "vcflib"]
	path = deps/vcflib
	url = https://github.com/vcflib/vcflib.git
[submodule "fastahack"]
	path = deps/fastahack
	url = https://github.com/vgteam/fastahack.git
[submodule "gssw"]
	path = deps/gssw
	url = https://github.com/ekg/gssw.git
[submodule "bash-tap"]
	path = deps/bash-tap
	url = https://github.com/illusori/bash-tap.git
[submodule "progress_bar"]
	path = deps/progress_bar
	url = https://github.com/vgteam/cpp_progress_bar.git
[submodule "lru_cache"]
	path = deps/lru_cache
	url = https://github.com/ekg/lru_cache.git
[submodule "htslib"]
	path = deps/htslib
	url = https://github.com/samtools/htslib.git
[submodule "sha1"]
	path = deps/sha1
	url = https://github.com/vog/sha1.git
[submodule "gcsa2"]
	path = deps/gcsa2
	url = https://github.com/jltsiren/gcsa2.git
[submodule "sdsl-lite"]
	path = deps/sdsl-lite
    url = https://github.com/simongog/sdsl-lite
[submodule "deps/libVCFH"]
	path = deps/libVCFH
	url = https://github.com/edawson/libVCFH.git
[submodule "deps/sparsehash"]
	path = deps/sparsehash
	url = https://github.com/sparsehash/sparsehash.git
[submodule "gfakluge"]
    path = deps/gfakluge
    url = https://github.com/vgteam/gfakluge.git
[submodule "deps/DYNAMIC"]
	path = deps/DYNAMIC
	url = https://github.com/vgteam/DYNAMIC
[submodule "deps/raptor"]
	path = deps/raptor
	url = https://github.com/vgteam/raptor.git
[submodule "deps/snappy"]
	path = deps/snappy
	url = https://github.com/google/snappy.git
[submodule "deps/Complete-Striped-Smith-Waterman-Library"]
	path = deps/ssw
	url = https://github.com/vgteam/Complete-Striped-Smith-Waterman-Library.git
[submodule "deps/pinchesAndCacti"]
	path = deps/pinchesAndCacti
	url = https://github.com/benedictpaten/pinchesAndCacti.git
[submodule "deps/sonLib"]
	path = deps/sonLib
	url = https://github.com/benedictpaten/sonLib.git
[submodule "deps/fermi-lite"]
	path = deps/fermi-lite
    url = https://github.com/edawson/fermi-lite.git
[submodule "deps/rocksdb"]
    path = deps/rocksdb
    url = https://github.com/facebook/rocksdb.git
[submodule "deps/gbwt"]
	path = deps/gbwt
	url = https://github.com/jltsiren/gbwt.git
[submodule "deps/sublinear-Li-Stephens"]
	path = deps/sublinear-Li-Stephens
	url = https://github.com/yoheirosen/sublinear-Li-Stephens.git
[submodule "deps/backward-cpp"]
	path = deps/backward-cpp
	url = https://github.com/adamnovak/backward-cpp.git
[submodule "deps/elfutils"]
	path = deps/elfutils
	url = git://sourceware.org/git/elfutils.git
[submodule "deps/structures"]
	path = deps/structures
	url = https://github.com/vgteam/structures.git
[submodule "deps/sparsepp"]
	path = deps/sparsepp
	url = https://github.com/greg7mdp/sparsepp.git
[submodule "deps/vowpal_wabbit"]
	path = deps/vowpal_wabbit
	url = https://github.com/JohnLangford/vowpal_wabbit.git
[submodule "deps/boost-subset"]
	path = deps/boost-subset
	url = https://github.com/vgteam/boost-subset.git
[submodule "deps/libdeflate"]
	path = deps/libdeflate
	url = https://github.com/ebiggers/libdeflate.git
[submodule "deps/dozeu"]
	path = deps/dozeu
	url = https://github.com/ocxtal/dozeu.git
[submodule "deps/libhandlegraph"]
	path = deps/libhandlegraph
	url = https://github.com/vgteam/libhandlegraph.git
[submodule "deps/libvgio"]
	path = deps/libvgio
	url = https://github.com/vgteam/libvgio.git
[submodule "deps/jemalloc"]
	path = deps/jemalloc
	url = https://github.com/jemalloc/jemalloc.git
[submodule "deps/sglib"]
	path = deps/sglib
	url = https://github.com/vgteam/sglib.git
	branch = master
[submodule "deps/FlameGraph"]
	path = deps/FlameGraph
	url = https://github.com/brendangregg/FlameGraph
[submodule "deps/libbdsg"]
	path = deps/libbdsg
	url = https://github.com/vgteam/libbdsg.git
[submodule "deps/xg"]
	path = deps/xg
	url = https://github.com/vgteam/xg.git
[submodule "deps/gbwtgraph"]
	path = deps/gbwtgraph
	url = https://github.com/jltsiren/gbwtgraph.git
[submodule "deps/ips4o"]
	path = deps/ips4o
	url = https://github.com/vgteam/ips4o.git
[submodule "deps/mmmultimap"]
	path = deps/mmmultimap
	url = https://github.com/ekg/mmmultimap.git
[submodule "vgteam_bbhash"]
	path = deps/BBHash
	url = https://github.com/vgteam/BBHash.git
