You can get a copy of GHC by downloading and installing the latest Haskell-platform.

For CentOS users, there is no binary distribution of Haskell platform available. Please follow these steps to install GHC and cabal:

1. Download GHC binary distribution.

2. Extract files: tar xf ghc-7.8.4-x86_64-unknown-linux-centos65.tar.bz2.

3. Read "INSTALL" file and follow the instruction to install GHC.

4. Download cabal-install-1.20.

5. tar zxf cabal-install-1.20.0.6.tar.gz && cd cabal-install-1.20.0.6 && ./bootstrap.sh.

6. add $HOME/.cabal/bin to your system searching path.

Open a terminal, type cabal update && cabal install alex && cabal install BCMtools.

After these steps, you will have the bcmtools executable in you cabal library directory. In Linux, this is typically under $HOME/.cabal/bin/. You can type bcmtools --help to get help information, and type bcmtools COMMAND --help to get more specific information.

BCMtools accept two types of input.

1. 3-column tsv. Example:

5000  \t 10000 \t  3.0
10000 \t 20000 \t  4.0
 .     .   .   .    .
 .     .   .   .    .
 .     .   .   .    .

This format is convenient for processing intra or inter chromosome contact maps. Every entries in the same column would then belong to the same chromsome.

2. 5-column tsv. Example:

chr1 \t 5000 \t chr2 \t 20000 \t 4.0
chr1 \t 5000 \t chr1 \t 30000 \t 2.0

To use BCMtools, we will need to convert text file to bcm files. bcm files are binary files which are designed to store huge matrix. This step will take 3-column/5-column tsv as input. Example:

bcmtools convert -g hg19 -s 100K -r chr1 -c chr1 -i input --symmetric -o 100K.bcm

Options:

• --symmetric: this tells BCMtools to store only half of the matrix.
• --sparse: if this flag is turn on, BCMtools will store the matrix as a Compressed Sparse Row (CSR) matrix. This will save huge amout of space when the matrix is very sparse. (Note: Sparse storage requires sorted input. We don't provide tools for sorting, yet. You can use unix sort to sort the input)

bcmtools view 100K.bcm --range 0-150 -o ouput.png

By default, BCMtools stores whole matrix in memory. If the --disk flag is turned on, BCMtools will perform all computation on disk, and only a tiny amount of data is stored in memory. This could be very useful when the matrix is large and memory is scarce.