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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++ 4.7 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 [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 executables are called bam-read and bam-split and will be in the src directory.

bam-split

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.

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