index_bam_by_read_id

python module for sorting, indexing and retrieving reads from BAMs using read IDs/names

installation

The simplest way to install the 'index_bam_by_read_id' module and the 'bam_reads_by_id' script is to use pip:

pip install index_bam_by_read_id

#or without root privileges 
pip install index_bam_by_read_id --user

Alternatively you may clone this repository with git and use the setup.py script:

git clone https://github.com/gantzgraf/index_bam_by_read_id.git
python setup.py install 
#or without root privileges
python setup.py install --user

pysam version 0.11.1 or higher is required.

bam_reads_by_id usage

The bundled script contains three main methods, 'sort', 'index' and 'get' in order to sort, index and retrieve records from a BAM. It can be used as follows:

bam_reads_by_id sort BAM [options]                                                     
bam_reads_by_id index BAM [options]    
bam_reads_by_id get BAM [options]      

For full documentation run:

bam_reads_by_id -h

Note that this program can output BAM, SAM and CRAM format when using the 'sort' and 'get' methods but only BAM and SAM formats can be indexed and be used as input for the 'get' command.

using the module

The index_bam_by_read_id module contains the the IndexByReadId module and two basic Exception classes (UnsortedBamError and OutFormatError). Documentation can be viewed from an interactive python session by running:

from index_bam_by_read_id import * 
help(IndexByReadId)