Installing (Development version)

git clone https://github.com/weng-lab/TwoBit.gitcd TwoBitgit checkout -b develop origin/develop #switch to develop branch#configure, compiler can be set or environmental CC and CXX will be usedCC=gcc-7 CXX=g++-7 ./configure.py #download cppitertools, cppprogutils./setup.py --compfile compfile.mk --outMakefile makefile-common.mk #compfile.mk created by configure#compilemake -j 4#binary now located in TwoBit/bin/bin/TwoBit#TwoBit#1) faToTwoBit#2) twoBitToFa

TODO

Example use

TwoBit::TwoBitFile f("/home/vanderva/.ucscgenome/hg19.2bit");std::string buffer;for (const std::string& s : f.sequenceNames()){f[s].getSequence(buffer);std::cout << ">" << s << std::endl;for (uint32_t i = 0; i < buffer.size(); i += 80){std::cout << buffer.substr(i, 80) << '\n';}std::cout.flush();}