CPP

Compiling

g++ -std=c++0x -o straw main.cpp straw.cpp -lcurl -lz

You must have cURL installed. Please see the wiki for more documentation.

For questions, please use the Google Group.

straw must be compiled with the -lz flag to include the zlib.h library:

On Linux, you may need to use this flag to compile: -std=c++11

On Windows, we've compiled using Cygwin. Order matters, put the linking libraries last:

g++ -o straw main.cpp straw.cpp -lz -std=c++11

Running

Usage:

straw <NONE/VC/VC_SQRT/KR> <hicFile> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize>

Extract all reads on chromosome X at 1MB resolution with no normalization in local file "HIC001.hic"

straw NONE HIC001.hic X X BP 1000000

Extract reads between 1MB and 7.5MB on chromosome 1 at 25KB resolution with KR (balanced) normalization:

straw KR HIC001.hic 1:1000000:7400000 1:1000000:7400000 BP 25000