phe.mapping.Bowtie2Mapper module

Implementation of the Mapper class using Bowtie2 mapper.

Date:17 Sep, 2015 Author:Alex Jironkin

class Bowtie2Mapper(cmd_options=None)

Bases: phe.mapping.Mapper

Bowtie2 mapper

Methods

create_aux_files(ref)
get_info([plain])
get_meta()
get_samtools_version()	Get version of samtools used.
get_version()
make_bam(*args, **kwargs)	Make indexed BAM from reference, and fastq files.
make_sam(*args, **kwargs)
validate()	Validate itself, by checking appropriate commands can run.

create_aux_files(ref)

get_info(plain=False)

get_version()

make_sam(*args, **kwargs)

name = 'bowtie2'

Plain text name of the mapper.