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

Packages that use fr.ens.biologie.genomique.eoulsan.modules.mapping

Package	Description
fr.ens.biologie.genomique.eoulsan.modules.mapping	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step.
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mapping.local	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in local mode.

Classes in fr.ens.biologie.genomique.eoulsan.modules.mapping used by fr.ens.biologie.genomique.eoulsan.modules.mapping

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

Classes in fr.ens.biologie.genomique.eoulsan.modules.mapping used by fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop

Class	Description
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.
AbstractSAMFilterModule	This class define an abstract module for alignments filtering.

Classes in fr.ens.biologie.genomique.eoulsan.modules.mapping used by fr.ens.biologie.genomique.eoulsan.modules.mapping.local

Class	Description
AbstractBAM2SAMModule	This class define a module for converting BAM files into SAM.
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.