Package fr.ens.biologie.genomique.eoulsan.data

Class DataFormats

java.lang.Object
fr.ens.biologie.genomique.eoulsan.data.DataFormats
public class DataFormats extends Object
This class contains the definition of some DataFormats.
Since:
1.0
Author:
Laurent Jourdren

  • Field Details

    • READS_FASTQ

      public static final DataFormat READS_FASTQ
      Reads fastq data format.

    • READS_TFQ

      public static final DataFormat READS_TFQ
      Reads tfq data format.

    • BWA_INDEX_ZIP

      public static final DataFormat BWA_INDEX_ZIP
      BWA index data format.

    • BOWTIE_INDEX_ZIP

      public static final DataFormat BOWTIE_INDEX_ZIP
      Bowtie index data format.

    • BOWTIE2_INDEX_ZIP

      public static final DataFormat BOWTIE2_INDEX_ZIP
      Bowtie2 index data format.

    • GSNAP_INDEX_ZIP

      public static final DataFormat GSNAP_INDEX_ZIP
      Gmap index data format.

    • STAR_INDEX_ZIP

      public static final DataFormat STAR_INDEX_ZIP
      STAR index data format.

    • MINIMAP2_INDEX_ZIP

      public static final DataFormat MINIMAP2_INDEX_ZIP
      Minimap2 index data format.

    • MAPPER_RESULTS_SAM

      public static final DataFormat MAPPER_RESULTS_SAM
      SAM results data format.

    • MAPPER_RESULTS_BAM

      public static final DataFormat MAPPER_RESULTS_BAM
      BAM results data format.

    • MAPPER_RESULTS_INDEX_BAI

      public static final DataFormat MAPPER_RESULTS_INDEX_BAI
      BAM index results data format.

    • MAPPER_RESULTS_LOG

      public static final DataFormat MAPPER_RESULTS_LOG
      Mapper log file format.

    • EXPRESSION_RESULTS_TSV

      public static final DataFormat EXPRESSION_RESULTS_TSV
      Expression results data format.

    • ANNOTATION_GFF

      public static final DataFormat ANNOTATION_GFF
      GFF data format.

    • ANNOTATION_GTF

      public static final DataFormat ANNOTATION_GTF
      GTF data format.

    • DIFFANA_RESULTS_TSV

      public static final DataFormat DIFFANA_RESULTS_TSV
      Diffana results data format.

    • GENOME_FASTA

      public static final DataFormat GENOME_FASTA
      Genome data format.

    • GENOME_DESC_TXT

      public static final DataFormat GENOME_DESC_TXT
      Genome data format.

    • UNMAP_READS_FASTA

      public static final DataFormat UNMAP_READS_FASTA
      Unmap reads results data format.

    • ANNOTATED_EXPRESSION_RESULTS_TSV

      public static final DataFormat ANNOTATED_EXPRESSION_RESULTS_TSV
      TSV Annotated expression results data format.

    • ANNOTATED_EXPRESSION_RESULTS_ODS

      public static final DataFormat ANNOTATED_EXPRESSION_RESULTS_ODS
      ODS Annotated expression results data format.

    • ANNOTATED_EXPRESSION_RESULTS_XLSX

      public static final DataFormat ANNOTATED_EXPRESSION_RESULTS_XLSX
      XLSX Annotated expression results data format.

    • ADDITIONAL_ANNOTATION_TSV

      public static final DataFormat ADDITIONAL_ANNOTATION_TSV
      Additional annotation data format.

    • FASTQC_REPORT_HTML

      public static final DataFormat FASTQC_REPORT_HTML
      FastQC HTML report format.

    • FASTQC_REPORT_ZIP

      public static final DataFormat FASTQC_REPORT_ZIP
      FastQC ZIP report format.

    • DUMMY_TXT

      public static final DataFormat DUMMY_TXT
      Dummy format.

    • BIGBED

      public static final DataFormat BIGBED
      BigBed format.

    • BIGWIG

      public static final DataFormat BIGWIG
      BigWig format.

    • CUTADAPT_ADAPTER_FASTA

      public static final DataFormat CUTADAPT_ADAPTER_FASTA
      Cutadapt adapters format.

    • MULTIQC_REPORT_HTML

      public static final DataFormat MULTIQC_REPORT_HTML
      MultiQC HTML report format.

    • FEATURECOUNTS_SUMMARY_TXT

      public static final DataFormat FEATURECOUNTS_SUMMARY_TXT
      FeatureCounts summary format.

    • EXPRESSION_MATRIX_TSV

      public static final DataFormat EXPRESSION_MATRIX_TSV
      Expression matrix.

    • SINGLE_CELL_EXPERMIMENT_RDS

      public static final DataFormat SINGLE_CELL_EXPERMIMENT_RDS
      R single cell experiment.

    • MAPPER_RESULT_BED

      public static final DataFormat MAPPER_RESULT_BED
      BED format.

  • Constructor Details

    • DataFormats

      public DataFormats()