Package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
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
-
ClassesClassDescriptionThis class define a Step that filter and map read in Hadoop mode.This class contains utility methods for the Hadoop mapping package classes.This class allow to convert two FASTQ file in one TFQ file.This class define the reducer required to convert FASTQ files into TFQ file.This class defines a mapper for the pretreatment of paired-end data before the reads filtering step.This class define a reducer for the pretreatment of paired-end data before the reads filtering step.This class is the main class for the filter reads program in hadoop mode.This class defines a read filter mapper.This class define an mapper module in Hadoop mode.This class defines a generic mapper for reads mapping.This class define a module for converting SAM files into BAM.This class define a filter alignment step in Hadoop mode.This class defines a mapper for alignment filtering.This class define a reducer for alignments filtering.This class contains methods and classes related to save and load SAM file header in Hadoop mappers and reducers.This class allow to save the SAM header read by a mapper.