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.