/*
* Eoulsan development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public License version 2.1 or
* later and CeCILL-C. This should be distributed with the code.
* If you do not have a copy, see:
*
* http://www.gnu.org/licenses/lgpl-2.1.txt
* http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
*
* Copyright for this code is held jointly by the Genomic platform
* of the Institut de Biologie de l'École normale supérieure and
* the individual authors. These should be listed in @author doc
* comments.
*
* For more information on the Eoulsan project and its aims,
* or to join the Eoulsan Google group, visit the home page
* at:
*
* http://outils.genomique.biologie.ens.fr/eoulsan
*
*/
package fr.ens.biologie.genomique.eoulsan.data;
/**
* This class contains the definition of some DataFormats.
* @since 1.0
* @author Laurent Jourdren
*/
public class DataFormats {
private static final DataFormatRegistry registry =
DataFormatRegistry.getInstance();
/** Reads fastq data format. */
public static final DataFormat READS_FASTQ =
registry.getDataFormatFromName("reads_fastq");
/** Reads tfq data format. */
public static final DataFormat READS_TFQ =
registry.getDataFormatFromName("reads_tfq");
/** BWA index data format. */
public static final DataFormat BWA_INDEX_ZIP =
registry.getDataFormatFromName("bwa_index_zip");
/** Bowtie index data format. */
public static final DataFormat BOWTIE_INDEX_ZIP =
registry.getDataFormatFromName("bowtie_index_zip");
/** Bowtie2 index data format. */
public static final DataFormat BOWTIE2_INDEX_ZIP =
registry.getDataFormatFromName("bowtie2_index_zip");
/** Gmap index data format. */
public static final DataFormat GSNAP_INDEX_ZIP =
registry.getDataFormatFromName("gsnap_index_zip");
/** STAR index data format. */
public static final DataFormat STAR_INDEX_ZIP =
registry.getDataFormatFromName("star_index_zip");
/** SAM results data format. */
public static final DataFormat MAPPER_RESULTS_SAM =
registry.getDataFormatFromName("mapper_results_sam");
/** BAM results data format. */
public static final DataFormat MAPPER_RESULTS_BAM =
registry.getDataFormatFromName("mapper_results_bam");
/** BAM index results data format. */
public static final DataFormat MAPPER_RESULTS_INDEX_BAI =
registry.getDataFormatFromName("mapper_results_index_bai");
/** Expression results data format. */
public static final DataFormat EXPRESSION_RESULTS_TSV =
registry.getDataFormatFromName("expression_results_tsv");
/** GFF data format. */
public static final DataFormat ANNOTATION_GFF =
registry.getDataFormatFromName("annotation_gff");
/** GTF data format. */
public static final DataFormat ANNOTATION_GTF =
registry.getDataFormatFromName("annotation_gtf");
/** Diffana results data format. */
public static final DataFormat DIFFANA_RESULTS_TSV =
registry.getDataFormatFromName("diffana_results_tsv");
/** Genome data format. */
public static final DataFormat GENOME_FASTA =
registry.getDataFormatFromName("genome_fasta");
/** Genome data format. */
public static final DataFormat GENOME_DESC_TXT =
registry.getDataFormatFromName("genome_desc_txt");
/** Unmap reads results data format. */
public static final DataFormat UNMAP_READS_FASTA =
registry.getDataFormatFromName("unmap_fasta");
/** TSV Annotated expression results data format. */
public static final DataFormat ANNOTATED_EXPRESSION_RESULTS_TSV =
registry.getDataFormatFromName("annotated_expression_results_tsv");
/** ODS Annotated expression results data format. */
public static final DataFormat ANNOTATED_EXPRESSION_RESULTS_ODS =
registry.getDataFormatFromName("annotated_expression_results_ods");
/** XLSX Annotated expression results data format. */
public static final DataFormat ANNOTATED_EXPRESSION_RESULTS_XLSX =
registry.getDataFormatFromName("annotated_expression_results_xlsx");
/** Additional annotation data format. */
public static final DataFormat ADDITIONAL_ANNOTATION_TSV =
registry.getDataFormatFromName("additional_annotation_tsv");
/** FastQC report format. */
public static final DataFormat FASTQC_REPORT_HTML =
registry.getDataFormatFromName("fastqc_report_html");
/** Dummy format. */
public static final DataFormat DUMMY_TXT =
registry.getDataFormatFromName("dummy_txt");
/** Cutadapt adapters format. */
public static final DataFormat CUTADAPT_ADAPTER_FASTA =
registry.getDataFormatFromName("cutadapt_adapter");
}