Command-line tools used by transrate for processing bam files. Written in C++ and using Bamtools.
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 [email protected]: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.
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