transrate-tools

Command-line tools used by transrate for processing bam files. Written in C++ and using Bamtools.

building

transrate-tools uses C++11 features, so you’ll need at least g++ 4.8 installed. On OSX you can install the latest gcc with brew install gcc49. Note that on OSX you always need to tell cmake where to find gcc, using the option -DCMAKE_CXX_COMPILER=$(which g++-4.9).

Make sure you clone with submodules:

$ git clone --recursive git@github.com:cboursnell/transrate-tools.git

And you’ll need cmake installed.

Next, build bamtools:

on linux:

$ cd bamtools
$ mkdir build
$ cd build
$ cmake ..
$ make
$ cd ../../

or on OSX:

$ cd bamtools
$ mkdir build
$ cd build
$ cmake -DCMAKE_CXX_COMPILER=$(which g++-4.9) ..
$ make
$ cd ../../

Then build transrate-tools…

on linux:

$ cmake .
$ make

on OSX:

$ cmake -DCMAKE_CXX_COMPILER=$(which g++-4.9) .
$ make

The executable is called bam-read and will be in the src directory.

bam-read

Parse bam files after multi-mapping reads have been assigned and aggregate read mapping information by contig.

Currently captured:

• name
• bases mapped
• edit distance
• bridges
• length
• reads mapped
• both mapped
• proper pair
• good
• uncovered bases
• mean mapq
• probability of coverage not being segmented