Package 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.

Since:

1.0

Class Summary

Class	Description
FilterAndMapReadsHadoopModule	This class define a Step that filter and map read in Hadoop mode.
HadoopBamUtils
HadoopMappingUtils	This class contains utility methods for the Hadoop mapping package classes.
PairedEndFastqToTfq	This class allow to convert two FASTQ file in one TFQ file.
PairedEndFastqToTfq.FastqPairedEndReducer	This class define the reducer required to convert FASTQ files into TFQ file.
PreTreatmentMapper	This class defines a mapper for the pretreatment of paired-end data before the reads filtering step.
PreTreatmentReducer	This class define a reducer for the pretreatment of paired-end data before the reads filtering step.
ReadsFilterHadoopModule	This class is the main class for the filter reads program in hadoop mode.
ReadsFilterMapper	This class defines a read filter mapper.
ReadsMapperHadoopModule	This class define an mapper module in Hadoop mode.
ReadsMapperMapper	This class defines a generic mapper for reads mapping.
SAM2BAMHadoopModule	This class define a module for converting SAM files into BAM.
SAMFilterHadoopModule	This class define a filter alignment step in Hadoop mode.
SAMFilterMapper	This class defines a mapper for alignment filtering.
SAMFilterReducer	This class define a reducer for alignments filtering.
SAMHeaderHadoopUtils	This class contains methods and classes related to save and load SAM file header in Hadoop mappers and reducers.
SAMHeaderHadoopUtils.SAMHeaderWriter	This class allow to save the SAM header read by a mapper.