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 Summary

Fields

Modifier and Type	Field	Description
static DataFormat	ADDITIONAL_ANNOTATION_TSV	Additional annotation data format.
static DataFormat	ANNOTATED_EXPRESSION_RESULTS_ODS	ODS Annotated expression results data format.
static DataFormat	ANNOTATED_EXPRESSION_RESULTS_TSV	TSV Annotated expression results data format.
static DataFormat	ANNOTATED_EXPRESSION_RESULTS_XLSX	XLSX Annotated expression results data format.
static DataFormat	ANNOTATION_GFF	GFF data format.
static DataFormat	ANNOTATION_GTF	GTF data format.
static DataFormat	BIGBED	BigBed format.
static DataFormat	BIGWIG	BigWig format.
static DataFormat	BOWTIE_INDEX_ZIP	Bowtie index data format.
static DataFormat	BOWTIE2_INDEX_ZIP	Bowtie2 index data format.
static DataFormat	BWA_INDEX_ZIP	BWA index data format.
static DataFormat	CUTADAPT_ADAPTER_FASTA	Cutadapt adapters format.
static DataFormat	DIFFANA_RESULTS_TSV	Diffana results data format.
static DataFormat	DUMMY_TXT	Dummy format.
static DataFormat	EXPRESSION_MATRIX_TSV	Expression matrix.
static DataFormat	EXPRESSION_RESULTS_TSV	Expression results data format.
static DataFormat	FASTQC_REPORT_HTML	FastQC HTML report format.
static DataFormat	FASTQC_REPORT_ZIP	FastQC ZIP report format.
static DataFormat	FEATURECOUNTS_SUMMARY_TXT	FeatureCounts summary format.
static DataFormat	GENOME_DESC_TXT	Genome data format.
static DataFormat	GENOME_FASTA	Genome data format.
static DataFormat	GSNAP_INDEX_ZIP	Gmap index data format.
static DataFormat	MAPPER_RESULT_BED	BED format.
static DataFormat	MAPPER_RESULTS_BAM	BAM results data format.
static DataFormat	MAPPER_RESULTS_INDEX_BAI	BAM index results data format.
static DataFormat	MAPPER_RESULTS_LOG	Mapper log file format.
static DataFormat	MAPPER_RESULTS_SAM	SAM results data format.
static DataFormat	MINIMAP2_INDEX_ZIP	Minimap2 index data format.
static DataFormat	MULTIQC_REPORT_HTML	MultiQC HTML report format.
static DataFormat	READS_FASTQ	Reads fastq data format.
static DataFormat	READS_TFQ	Reads tfq data format.
static DataFormat	SINGLE_CELL_EXPERMIMENT_RDS	R single cell experiment.
static DataFormat	STAR_INDEX_ZIP	STAR index data format.
static DataFormat	UNMAP_READS_FASTA	Unmap reads results data format.

Constructor Summary

Constructors

Constructor	Description
DataFormats()

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

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 Detail

DataFormats

public DataFormats()