2-bit reader/writer

Version 2.0.9

This is a (work in progress) reader implementation, based on thespecs at UCSC, http://genome.ucsc.edu/FAQ/FAQformat#format7. Theimplementation is intended to be more or less thread safe; to achievethat, each TwoBitSequence has it’s own read-only file handle to the 2-bitdata.

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

• probably take out buffering and rely on ifstream, see https://stackoverflow.com/questions/12757904/how-to-optimize-reading-and-writing-by-playing-with-buffer-size.
• make TwoBitSequence in input stream? https://stackoverflow.com/questions/14086417/how-to-write-custom-input-stream-in-c

Example use

The following converts a 2-bit file into FASTA format, on stdout.

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();}

keywords: UCSC, twobit, 2bit, genome, file format, reader, writer, parser, zlab, Weng Lab, Arjan van der Velde, Nick Hathaway