Package fr.ens.biologie.genomique.eoulsan.modules.mapping

This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step.

Since:

1.0

Class Summary

Class	Description
AbstractBAM2SAMModule	This class define a module for converting BAM files into SAM.
AbstractFilterAndMapReadsModule	This class define an abstract module for read filtering, mapping and alignments filtering.
AbstractReadsFilterModule	This class define an abstract module for read filtering.
AbstractReadsMapperModule	This class define an abstract module for read mapping.
AbstractSAM2BAMModule	This class define a module for converting SAM files into BAM.
AbstractSAM2FASTQModule	This class define a module for converting SAM files into BAM.
AbstractSAMFilterModule	This class define an abstract module for alignments filtering.
AbstractSplice2BEDModule	This class define a module for converting SAM files into BED.

Enum Summary

Enum	Description
MappingCounters	This enum define the names of the counters of the steps of this package.