Reading bam files and aggregating read mapping information about sequences
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bamtools @ 2d7685d


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++ 4.7 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

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 executables are called bam-read and bam-split and will be in the src directory.


Parse bam files to separate records that will be filtered by eXpress so that they can be merged back in to the sampled assignments for multi-mapping reads.


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