java.lang.Object
- fr.ens.biologie.genomique.aozan.Settings

```
public final class Settings
extends Object
```
This class define constants to keys of configuration Aozan file.

Since:

1.2.1

Author:

Sandrine Perrin

Field Summary

Fields
Modifier and Type	Field	Description
`static String`	`AOZAN_CONF_FILE_PATH`
`static String`	`AOZAN_DEBUG_KEY`	Mode Aozan debug.
`static String`	`AOZAN_ENABLE_KEY`	Aozan enable.
`static String`	`AOZAN_LOG_LEVEL_KEY`	Aozan log level.
`static String`	`AOZAN_LOG_PATH_KEY`	Aozan log path.
`static String`	`AOZAN_VAR_PATH_KEY`	Aozan directory var path.
`static String`	`BCL_DATA_PATH_KEY`	Aozan directory bcl path.
`static String`	`BCL_SPACE_FACTOR_KEY`	Aozan bcl space factor.
`static String`	`BCL2FASTQ_ADAPTER_FASTA_FILE_PATH_KEY`	Blc2fastq adapter fasta file path.
`static String`	`BCL2FASTQ_ADDITIONNAL_ARGUMENTS_KEY`	Blc2fastq additionnal arguments.
`static String`	`BCL2FASTQ_COMPRESSION_KEY`	Bcl2fastq compression fastq files.
`static String`	`BCL2FASTQ_COMPRESSION_LEVEL_KEY`	Bcl2fastq compression level.
`static String`	`BCL2FASTQ_FASTQ_CLUSTER_COUNT_KEY`	Bcl2fastq fastq cluster count.
`static String`	`BCL2FASTQ_MISMATCHES_KEY`	Bcl2fastq mismatches.
`static String`	`BCL2FASTQ_PATH_KEY`	Bcl2fastq path.
`static String`	`BCL2FASTQ_USE_DOCKER_KEY`	Set available use container docker.
`static String`	`BCL2FASTQ_WITH_FAILED_READS_KEY`	Bcl2fastq with failed reads.
`static String`	`DEMUX_ARCHIVE_SAMPLESHEETS_KEY`	Archive samplesheets key.
`static String`	`DEMUX_SPACE_FACTOR_KEY`	Demultiplex space factor.
`static String`	`DEMUX_STEP_KEY`	Demultiplex step.
`static String`	`DEMUX_THREADS_KEY`	Bcl2fastq threads.
`static String`	`DEMUX_USE_HISEQ_OUTPUT_KEY`	Demultiplex use Hiseq output.
`static String`	`DOCKER_URI_KEY`	Docker connection string.
`static String`	`FASTQ_DATA_PATH_KEY`	Fastq directory data path.
`static String`	`FASTQ_SPACE_FACTOR_KEY`	Fastq space factor.
`static String`	`FIRST_BASE_REPORT_STEP_KEY`	First base report step.
`static String`	`HISEQ_CRITICAL_MIN_SPACE_KEY`	Hiseq critical minimum space.
`static String`	`HISEQ_DATA_PATH_KEY`	hiseq directory data path.
`static String`	`HISEQ_SPACE_FACTOR_KEY`	Hiseq space factor.
`static String`	`HISEQ_STEP_KEY`	Hiseq step.
`static String`	`HISEQ_WARNING_MIN_SPACE_KEY`	Hiseq warning minimum space.
`static String`	`INDEX_HTML_TEMPLATE_KEY`	Index html template path.
`static String`	`INDEX_SEQUENCES_KEY`	Index sequences path.
`static String`	`LOCK_FILE_KEY`	Lock file.
`static String`	`MAIL_ERROR_TO_KEY`	Mail error to.
`static String`	`MAIL_FOOTER_KEY`	Mail footer.
`static String`	`MAIL_FROM_KEY`	Mail from.
`static String`	`MAIL_HEADER_KEY`	Mail header.
`static String`	`MAIL_TO_KEY`	Mail to.
`static String`	`QC_CONF_FASTQC_ADAPTER_FILE_KEY`	Path to a specific adapter file, replace default file.
`static String`	`QC_CONF_FASTQC_BLAST_ARGUMENTS_KEY`	Collector fastqscreen blast arguments.
`static String`	`QC_CONF_FASTQC_BLAST_DB_PATH_KEY`	Collector FastQC blast database path.
`static String`	`QC_CONF_FASTQC_BLAST_ENABLE_KEY`	Collector FastQC blast enable.
`static String`	`QC_CONF_FASTQC_BLAST_PATH_KEY`	Collector FastQC blast path.
`static String`	`QC_CONF_FASTQC_BLAST_USE_DOCKER_KEY`	Use Docker for Blast.
`static String`	`QC_CONF_FASTQC_CASAVA_KEY`	Illumina FASTQ format for FastQC.
`static String`	`QC_CONF_FASTQC_CONTAMINANT_FILE_KEY`	Collector FastQC contaminant file.
`static String`	`QC_CONF_FASTQC_EXPGROUP_KEY`	Use exponential base groups in graph.
`static String`	`QC_CONF_FASTQC_KEEP_ZIP_REPORT_FILE_KEY`	Collector FastQC, keep zip report file.
`static String`	`QC_CONF_FASTQC_KMER_SIZE_KEY`	Collector FastQC kmer size.
`static String`	`QC_CONF_FASTQC_LIMITS_FILE_KEY`	Path to a specific limits file, replace default file.
`static String`	`QC_CONF_FASTQC_NANO_KEY`	New option with FastQC 0.11.3 to nanopore technology, use Fast5 file instead of FastQ
`static String`	`QC_CONF_FASTQC_NOFILTER_KEY`	Filter bad Illumina FASTQ entry in FastQC.
`static String`	`QC_CONF_FASTQC_NOGROUP_KEY`	Collector FastQC nogroup.
`static String`	`QC_CONF_FASTQC_PROCESS_UNDETERMINED_SAMPLES_KEY`	Collector FastQC, process on undetermined indices samples, default at false.
`static String`	`QC_CONF_FASTQC_UNZIP_REPORT_FILE_KEY`	Collector FastQC, unzip report file.
`static String`	`QC_CONF_FASTQSCREEN_FASTQ_MAX_READS_PARSED_KEY`	Collector fastqscreen fastq max reads parsed.
`static String`	`QC_CONF_FASTQSCREEN_FASTQ_READS_PF_USED_KEY`	Collector fastqscreen fastq reads pf used.
`static String`	`QC_CONF_FASTQSCREEN_GENOMES_ALIAS_PATH_KEY`	Collector fastqscreen settings genomes alias path.
`static String`	`QC_CONF_FASTQSCREEN_GENOMES_DESC_PATH_KEY`	Collector fastqscreen settings genomes description path.
`static String`	`QC_CONF_FASTQSCREEN_GENOMES_KEY`	Collector fastqscreen genomes.
`static String`	`QC_CONF_FASTQSCREEN_GENOMES_PATH_KEY`	Collector fastqscreen settings genomes.
`static String`	`QC_CONF_FASTQSCREEN_MAPPER_ARGUMENTS_KEY`	Collector fastqscreen mapper argument.
`static String`	`QC_CONF_FASTQSCREEN_MAPPER_KEY`	Collector fastqscreen mapper.
`static String`	`QC_CONF_FASTQSCREEN_MAPPERS_INDEXES_PATH_KEY`	Collector fastqscreen settings mappers indexes path.
`static String`	`QC_CONF_FASTQSCREEN_MAPPING_IGNORE_PAIRED_END_MODE_KEY`	Collector fastqscreen mapping ignore paired mode.
`static String`	`QC_CONF_FASTQSCREEN_MAPPING_SKIP_CONTROL_LANE_KEY`	Collector fastqscreen mapping skip control lane.
`static String`	`QC_CONF_FASTQSCREEN_MAX_READ_LENGTH_KEY`	Collector fastqscreen settings max read length.
`static String`	`QC_CONF_FASTQSCREEN_PERCENT_PROJECT_CONTAMINATION_THRESHOLD_KEY`	Collector project, fastqscreen xsl file
`static String`	`QC_CONF_FASTQSCREEN_PROCESS_UNDETERMINED_SAMPLES_KEY`	Collector FastqScreen, process on undetermined indices samples, default at false.
`static String`	`QC_CONF_FASTQSCREEN_PROJECT_XSL_FILE_KEY`	Collector project, fastqscreen xsl file
`static String`	`QC_CONF_FASTQSCREEN_XSL_FILE_KEY`	Collector fastqscreen xsl file.
`static String`	`QC_CONF_MULTIQC_USE_DOCKER_KEY`	Use Docker for MultiQC.
`static String`	`QC_CONF_READ_XML_COLLECTOR_USED_KEY`	Collector read xml collector used.
`static String`	`QC_CONF_THREADS_KEY`	Collector threads.
`static String`	`QC_CONF_UNDETERMINED_INDEXED_XSL_FILE_KEY`	Collector undetermined indexed xsl file.
`static String`	`QC_REPORT_SAVE_RAW_DATA_KEY`	QC report save raw data.
`static String`	`QC_REPORT_SAVE_REPORT_DATA_KEY`	QC report save report data.
`static String`	`QC_REPORT_STYLESHEET_KEY`	QC report stylesheet path.
`static String`	`QC_STEP_KEY`	QC step.
`static String`	`READ_ONLY_OUTPUT_FILES_KEY`	Change the output file rights.
`static String`	`RECOMPRESS_COMPRESSION_KEY`	Erase input after recompression.
`static String`	`RECOMPRESS_COMPRESSION_LEVEL_KEY`	Erase input after recompression.
`static String`	`RECOMPRESS_DELETE_ORIGINAL_FASTQ_KEY`	Erase input after recompression.
`static String`	`RECOMPRESS_STEP_KEY`	Recompression step.
`static String`	`RECOMPRESS_THREADS_KEY`	Erase input after recompression.
`static String`	`REPORTS_DATA_PATH_KEY`	Report directory data path.
`static String`	`REPORTS_URL_KEY`	Report url.
`static String`	`SAMPLESHEET_FORMAT_KEY`	Bcl2fastq samplesheet format.
`static String`	`SAMPLESHEET_GENERATOR_COMMAND_KEY`	Bcl2fastq samplesheet generator command.
`static String`	`SAMPLESHEET_PATH_KEY`	Bcl2fastq samplesheet path.
`static String`	`SAMPLESHEET_PREFIX_KEY`	Bcl2fastq samplesheet prefix filename.
`static String`	`SEND_MAIL_KEY`	Send mail.
`static String`	`SYNC_CONTINUOUS_SYNC_KEY`	Synchronization continuous.
`static String`	`SYNC_CONTINUOUS_SYNC_MIN_AGE_FILES_KEY`	Synchronization continuous minimum ages files.
`static String`	`SYNC_EXCLUDE_CIF_KEY`	Synchronization exclude cif files.
`static String`	`SYNC_SPACE_FACTOR_KEY`	Synchronization space factor.
`static String`	`SYNC_STEP_KEY`	Synchronization step.
`static String`	`TMP_PATH_KEY`	Directory tmp path.

Constructor Summary

Constructors
Constructor Description

Settings(Map<String,String> map)
Public constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`containsKey(String key)`	Test if the settings contains a key.
`Set<Map.Entry<String,String>>`	`entrySet()`	Get an entry set of the setting values.
`String`	`get(String key)`	Get a setting value.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - AOZAN_DEBUG_KEY
```
public static final String AOZAN_DEBUG_KEY
```
    Mode Aozan debug.
    
    See Also:
    
    Constant Field Values
  - AOZAN_ENABLE_KEY
```
public static final String AOZAN_ENABLE_KEY
```
    Aozan enable.
    
    See Also:
    
    Constant Field Values
  - AOZAN_LOG_LEVEL_KEY
```
public static final String AOZAN_LOG_LEVEL_KEY
```
    Aozan log level.
    
    See Also:
    
    Constant Field Values
  - AOZAN_LOG_PATH_KEY
```
public static final String AOZAN_LOG_PATH_KEY
```
    Aozan log path.
    
    See Also:
    
    Constant Field Values
  - AOZAN_VAR_PATH_KEY
```
public static final String AOZAN_VAR_PATH_KEY
```
    Aozan directory var path.
    
    See Also:
    
    Constant Field Values
  - AOZAN_CONF_FILE_PATH
```
public static final String AOZAN_CONF_FILE_PATH
```
    See Also:
    
    Constant Field Values
  - BCL_DATA_PATH_KEY
```
public static final String BCL_DATA_PATH_KEY
```
    Aozan directory bcl path.
    
    See Also:
    
    Constant Field Values
  - BCL_SPACE_FACTOR_KEY
```
public static final String BCL_SPACE_FACTOR_KEY
```
    Aozan bcl space factor.
    
    See Also:
    
    Constant Field Values
  - HISEQ_CRITICAL_MIN_SPACE_KEY
```
public static final String HISEQ_CRITICAL_MIN_SPACE_KEY
```
    Hiseq critical minimum space.
    
    See Also:
    
    Constant Field Values
  - HISEQ_DATA_PATH_KEY
```
public static final String HISEQ_DATA_PATH_KEY
```
    hiseq directory data path.
    
    See Also:
    
    Constant Field Values
  - HISEQ_SPACE_FACTOR_KEY
```
public static final String HISEQ_SPACE_FACTOR_KEY
```
    Hiseq space factor.
    
    See Also:
    
    Constant Field Values
  - HISEQ_STEP_KEY
```
public static final String HISEQ_STEP_KEY
```
    Hiseq step.
    
    See Also:
    
    Constant Field Values
  - HISEQ_WARNING_MIN_SPACE_KEY
```
public static final String HISEQ_WARNING_MIN_SPACE_KEY
```
    Hiseq warning minimum space.
    
    See Also:
    
    Constant Field Values
  - BCL2FASTQ_ADAPTER_FASTA_FILE_PATH_KEY
```
public static final String BCL2FASTQ_ADAPTER_FASTA_FILE_PATH_KEY
```
    Blc2fastq adapter fasta file path.
    
    See Also:
    
    Constant Field Values
  - BCL2FASTQ_ADDITIONNAL_ARGUMENTS_KEY
```
public static final String BCL2FASTQ_ADDITIONNAL_ARGUMENTS_KEY
```
    Blc2fastq additionnal arguments.
    
    See Also:
    
    Constant Field Values
  - BCL2FASTQ_COMPRESSION_KEY
```
public static final String BCL2FASTQ_COMPRESSION_KEY
```
    Bcl2fastq compression fastq files.
    
    See Also:
    
    Constant Field Values
  - BCL2FASTQ_COMPRESSION_LEVEL_KEY
```
public static final String BCL2FASTQ_COMPRESSION_LEVEL_KEY
```
    Bcl2fastq compression level.
    
    See Also:
    
    Constant Field Values
  - BCL2FASTQ_FASTQ_CLUSTER_COUNT_KEY
```
public static final String BCL2FASTQ_FASTQ_CLUSTER_COUNT_KEY
```
    Bcl2fastq fastq cluster count.
    
    See Also:
    
    Constant Field Values
  - BCL2FASTQ_MISMATCHES_KEY
```
public static final String BCL2FASTQ_MISMATCHES_KEY
```
    Bcl2fastq mismatches.
    
    See Also:
    
    Constant Field Values
  - BCL2FASTQ_PATH_KEY
```
public static final String BCL2FASTQ_PATH_KEY
```
    Bcl2fastq path.
    
    See Also:
    
    Constant Field Values
  - SAMPLESHEET_FORMAT_KEY
```
public static final String SAMPLESHEET_FORMAT_KEY
```
    Bcl2fastq samplesheet format.
    
    See Also:
    
    Constant Field Values
  - SAMPLESHEET_PREFIX_KEY
```
public static final String SAMPLESHEET_PREFIX_KEY
```
    Bcl2fastq samplesheet prefix filename.
    
    See Also:
    
    Constant Field Values
  - SAMPLESHEET_PATH_KEY
```
public static final String SAMPLESHEET_PATH_KEY
```
    Bcl2fastq samplesheet path.
    
    See Also:
    
    Constant Field Values
  - DEMUX_THREADS_KEY
```
public static final String DEMUX_THREADS_KEY
```
    Bcl2fastq threads.
    
    See Also:
    
    Constant Field Values
  - BCL2FASTQ_WITH_FAILED_READS_KEY
```
public static final String BCL2FASTQ_WITH_FAILED_READS_KEY
```
    Bcl2fastq with failed reads.
    
    See Also:
    
    Constant Field Values
  - SAMPLESHEET_GENERATOR_COMMAND_KEY
```
public static final String SAMPLESHEET_GENERATOR_COMMAND_KEY
```
    Bcl2fastq samplesheet generator command.
    
    See Also:
    
    Constant Field Values
  - BCL2FASTQ_USE_DOCKER_KEY
```
public static final String BCL2FASTQ_USE_DOCKER_KEY
```
    Set available use container docker.
    
    See Also:
    
    Constant Field Values
  - DEMUX_ARCHIVE_SAMPLESHEETS_KEY
```
public static final String DEMUX_ARCHIVE_SAMPLESHEETS_KEY
```
    Archive samplesheets key.
    
    See Also:
    
    Constant Field Values
  - DEMUX_SPACE_FACTOR_KEY
```
public static final String DEMUX_SPACE_FACTOR_KEY
```
    Demultiplex space factor.
    
    See Also:
    
    Constant Field Values
  - DEMUX_STEP_KEY
```
public static final String DEMUX_STEP_KEY
```
    Demultiplex step.
    
    See Also:
    
    Constant Field Values
  - DEMUX_USE_HISEQ_OUTPUT_KEY
```
public static final String DEMUX_USE_HISEQ_OUTPUT_KEY
```
    Demultiplex use Hiseq output.
    
    See Also:
    
    Constant Field Values
  - FASTQ_DATA_PATH_KEY
```
public static final String FASTQ_DATA_PATH_KEY
```
    Fastq directory data path.
    
    See Also:
    
    Constant Field Values
  - FASTQ_SPACE_FACTOR_KEY
```
public static final String FASTQ_SPACE_FACTOR_KEY
```
    Fastq space factor.
    
    See Also:
    
    Constant Field Values
  - FIRST_BASE_REPORT_STEP_KEY
```
public static final String FIRST_BASE_REPORT_STEP_KEY
```
    First base report step.
    
    See Also:
    
    Constant Field Values
  - RECOMPRESS_STEP_KEY
```
public static final String RECOMPRESS_STEP_KEY
```
    Recompression step.
    
    See Also:
    
    Constant Field Values
  - RECOMPRESS_DELETE_ORIGINAL_FASTQ_KEY
```
public static final String RECOMPRESS_DELETE_ORIGINAL_FASTQ_KEY
```
    Erase input after recompression.
    
    See Also:
    
    Constant Field Values
  - RECOMPRESS_COMPRESSION_LEVEL_KEY
```
public static final String RECOMPRESS_COMPRESSION_LEVEL_KEY
```
    Erase input after recompression.
    
    See Also:
    
    Constant Field Values
  - RECOMPRESS_THREADS_KEY
```
public static final String RECOMPRESS_THREADS_KEY
```
    Erase input after recompression.
    
    See Also:
    
    Constant Field Values
  - RECOMPRESS_COMPRESSION_KEY
```
public static final String RECOMPRESS_COMPRESSION_KEY
```
    Erase input after recompression.
    
    See Also:
    
    Constant Field Values
  - READ_ONLY_OUTPUT_FILES_KEY
```
public static final String READ_ONLY_OUTPUT_FILES_KEY
```
    Change the output file rights.
    
    See Also:
    
    Constant Field Values
  - INDEX_HTML_TEMPLATE_KEY
```
public static final String INDEX_HTML_TEMPLATE_KEY
```
    Index html template path.
    
    See Also:
    
    Constant Field Values
  - INDEX_SEQUENCES_KEY
```
public static final String INDEX_SEQUENCES_KEY
```
    Index sequences path.
    
    See Also:
    
    Constant Field Values
  - LOCK_FILE_KEY
```
public static final String LOCK_FILE_KEY
```
    Lock file.
    
    See Also:
    
    Constant Field Values
  - MAIL_ERROR_TO_KEY
```
public static final String MAIL_ERROR_TO_KEY
```
    Mail error to.
    
    See Also:
    
    Constant Field Values
  - MAIL_FOOTER_KEY
```
public static final String MAIL_FOOTER_KEY
```
    Mail footer.
    
    See Also:
    
    Constant Field Values
  - MAIL_FROM_KEY
```
public static final String MAIL_FROM_KEY
```
    Mail from.
    
    See Also:
    
    Constant Field Values
  - MAIL_HEADER_KEY
```
public static final String MAIL_HEADER_KEY
```
    Mail header.
    
    See Also:
    
    Constant Field Values
  - MAIL_TO_KEY
```
public static final String MAIL_TO_KEY
```
    Mail to.
    
    See Also:
    
    Constant Field Values
  - QC_REPORT_SAVE_RAW_DATA_KEY
```
public static final String QC_REPORT_SAVE_RAW_DATA_KEY
```
    QC report save raw data.
    
    See Also:
    
    Constant Field Values
  - QC_REPORT_SAVE_REPORT_DATA_KEY
```
public static final String QC_REPORT_SAVE_REPORT_DATA_KEY
```
    QC report save report data.
    
    See Also:
    
    Constant Field Values
  - QC_REPORT_STYLESHEET_KEY
```
public static final String QC_REPORT_STYLESHEET_KEY
```
    QC report stylesheet path.
    
    See Also:
    
    Constant Field Values
  - QC_STEP_KEY
```
public static final String QC_STEP_KEY
```
    QC step.
    
    See Also:
    
    Constant Field Values
  - REPORTS_DATA_PATH_KEY
```
public static final String REPORTS_DATA_PATH_KEY
```
    Report directory data path.
    
    See Also:
    
    Constant Field Values
  - REPORTS_URL_KEY
```
public static final String REPORTS_URL_KEY
```
    Report url.
    
    See Also:
    
    Constant Field Values
  - SEND_MAIL_KEY
```
public static final String SEND_MAIL_KEY
```
    Send mail.
    
    See Also:
    
    Constant Field Values
  - SYNC_CONTINUOUS_SYNC_KEY
```
public static final String SYNC_CONTINUOUS_SYNC_KEY
```
    Synchronization continuous.
    
    See Also:
    
    Constant Field Values
  - SYNC_CONTINUOUS_SYNC_MIN_AGE_FILES_KEY
```
public static final String SYNC_CONTINUOUS_SYNC_MIN_AGE_FILES_KEY
```
    Synchronization continuous minimum ages files.
    
    See Also:
    
    Constant Field Values
  - SYNC_EXCLUDE_CIF_KEY
```
public static final String SYNC_EXCLUDE_CIF_KEY
```
    Synchronization exclude cif files.
    
    See Also:
    
    Constant Field Values
  - SYNC_SPACE_FACTOR_KEY
```
public static final String SYNC_SPACE_FACTOR_KEY
```
    Synchronization space factor.
    
    See Also:
    
    Constant Field Values
  - SYNC_STEP_KEY
```
public static final String SYNC_STEP_KEY
```
    Synchronization step.
    
    See Also:
    
    Constant Field Values
  - TMP_PATH_KEY
```
public static final String TMP_PATH_KEY
```
    Directory tmp path.
    
    See Also:
    
    Constant Field Values
  - DOCKER_URI_KEY
```
public static final String DOCKER_URI_KEY
```
    Docker connection string.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_CONTAMINANT_FILE_KEY
```
public static final String QC_CONF_FASTQC_CONTAMINANT_FILE_KEY
```
    Collector FastQC contaminant file.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_KMER_SIZE_KEY
```
public static final String QC_CONF_FASTQC_KMER_SIZE_KEY
```
    Collector FastQC kmer size.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_NOGROUP_KEY
```
public static final String QC_CONF_FASTQC_NOGROUP_KEY
```
    Collector FastQC nogroup.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_ADAPTER_FILE_KEY
```
public static final String QC_CONF_FASTQC_ADAPTER_FILE_KEY
```
    Path to a specific adapter file, replace default file.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_LIMITS_FILE_KEY
```
public static final String QC_CONF_FASTQC_LIMITS_FILE_KEY
```
    Path to a specific limits file, replace default file.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_EXPGROUP_KEY
```
public static final String QC_CONF_FASTQC_EXPGROUP_KEY
```
    Use exponential base groups in graph.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_CASAVA_KEY
```
public static final String QC_CONF_FASTQC_CASAVA_KEY
```
    Illumina FASTQ format for FastQC.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_NOFILTER_KEY
```
public static final String QC_CONF_FASTQC_NOFILTER_KEY
```
    Filter bad Illumina FASTQ entry in FastQC.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_NANO_KEY
```
public static final String QC_CONF_FASTQC_NANO_KEY
```
    New option with FastQC 0.11.3 to nanopore technology, use Fast5 file instead of FastQ
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_BLAST_ARGUMENTS_KEY
```
public static final String QC_CONF_FASTQC_BLAST_ARGUMENTS_KEY
```
    Collector fastqscreen blast arguments.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_BLAST_DB_PATH_KEY
```
public static final String QC_CONF_FASTQC_BLAST_DB_PATH_KEY
```
    Collector FastQC blast database path.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_BLAST_ENABLE_KEY
```
public static final String QC_CONF_FASTQC_BLAST_ENABLE_KEY
```
    Collector FastQC blast enable.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_BLAST_PATH_KEY
```
public static final String QC_CONF_FASTQC_BLAST_PATH_KEY
```
    Collector FastQC blast path.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_BLAST_USE_DOCKER_KEY
```
public static final String QC_CONF_FASTQC_BLAST_USE_DOCKER_KEY
```
    Use Docker for Blast.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_FASTQ_MAX_READS_PARSED_KEY
```
public static final String QC_CONF_FASTQSCREEN_FASTQ_MAX_READS_PARSED_KEY
```
    Collector fastqscreen fastq max reads parsed.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_FASTQ_READS_PF_USED_KEY
```
public static final String QC_CONF_FASTQSCREEN_FASTQ_READS_PF_USED_KEY
```
    Collector fastqscreen fastq reads pf used.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_GENOMES_KEY
```
public static final String QC_CONF_FASTQSCREEN_GENOMES_KEY
```
    Collector fastqscreen genomes.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_MAPPER_KEY
```
public static final String QC_CONF_FASTQSCREEN_MAPPER_KEY
```
    Collector fastqscreen mapper.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_MAPPER_ARGUMENTS_KEY
```
public static final String QC_CONF_FASTQSCREEN_MAPPER_ARGUMENTS_KEY
```
    Collector fastqscreen mapper argument.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_MAPPING_IGNORE_PAIRED_END_MODE_KEY
```
public static final String QC_CONF_FASTQSCREEN_MAPPING_IGNORE_PAIRED_END_MODE_KEY
```
    Collector fastqscreen mapping ignore paired mode.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_MAPPING_SKIP_CONTROL_LANE_KEY
```
public static final String QC_CONF_FASTQSCREEN_MAPPING_SKIP_CONTROL_LANE_KEY
```
    Collector fastqscreen mapping skip control lane.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_GENOMES_PATH_KEY
```
public static final String QC_CONF_FASTQSCREEN_GENOMES_PATH_KEY
```
    Collector fastqscreen settings genomes.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_GENOMES_ALIAS_PATH_KEY
```
public static final String QC_CONF_FASTQSCREEN_GENOMES_ALIAS_PATH_KEY
```
    Collector fastqscreen settings genomes alias path.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_GENOMES_DESC_PATH_KEY
```
public static final String QC_CONF_FASTQSCREEN_GENOMES_DESC_PATH_KEY
```
    Collector fastqscreen settings genomes description path.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_MAPPERS_INDEXES_PATH_KEY
```
public static final String QC_CONF_FASTQSCREEN_MAPPERS_INDEXES_PATH_KEY
```
    Collector fastqscreen settings mappers indexes path.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_MAX_READ_LENGTH_KEY
```
public static final String QC_CONF_FASTQSCREEN_MAX_READ_LENGTH_KEY
```
    Collector fastqscreen settings max read length.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_XSL_FILE_KEY
```
public static final String QC_CONF_FASTQSCREEN_XSL_FILE_KEY
```
    Collector fastqscreen xsl file.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_PROJECT_XSL_FILE_KEY
```
public static final String QC_CONF_FASTQSCREEN_PROJECT_XSL_FILE_KEY
```
    Collector project, fastqscreen xsl file
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_PERCENT_PROJECT_CONTAMINATION_THRESHOLD_KEY
```
public static final String QC_CONF_FASTQSCREEN_PERCENT_PROJECT_CONTAMINATION_THRESHOLD_KEY
```
    Collector project, fastqscreen xsl file
    
    See Also:
    
    Constant Field Values
  - QC_CONF_MULTIQC_USE_DOCKER_KEY
```
public static final String QC_CONF_MULTIQC_USE_DOCKER_KEY
```
    Use Docker for MultiQC.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_READ_XML_COLLECTOR_USED_KEY
```
public static final String QC_CONF_READ_XML_COLLECTOR_USED_KEY
```
    Collector read xml collector used.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_THREADS_KEY
```
public static final String QC_CONF_THREADS_KEY
```
    Collector threads.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_UNDETERMINED_INDEXED_XSL_FILE_KEY
```
public static final String QC_CONF_UNDETERMINED_INDEXED_XSL_FILE_KEY
```
    Collector undetermined indexed xsl file.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_PROCESS_UNDETERMINED_SAMPLES_KEY
```
public static final String QC_CONF_FASTQC_PROCESS_UNDETERMINED_SAMPLES_KEY
```
    Collector FastQC, process on undetermined indices samples, default at false.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_UNZIP_REPORT_FILE_KEY
```
public static final String QC_CONF_FASTQC_UNZIP_REPORT_FILE_KEY
```
    Collector FastQC, unzip report file.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQC_KEEP_ZIP_REPORT_FILE_KEY
```
public static final String QC_CONF_FASTQC_KEEP_ZIP_REPORT_FILE_KEY
```
    Collector FastQC, keep zip report file.
    
    See Also:
    
    Constant Field Values
  - QC_CONF_FASTQSCREEN_PROCESS_UNDETERMINED_SAMPLES_KEY
```
public static final String QC_CONF_FASTQSCREEN_PROCESS_UNDETERMINED_SAMPLES_KEY
```
    Collector FastqScreen, process on undetermined indices samples, default at false.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Settings
```
public Settings(Map<String,String> map)
```
    Public constructor.
    
    Parameters:
    
    map - Aozan configuration
- Method Detail
  - get
```
public String get(String key)
```
    Get a setting value.
    
    Parameters:
    
    key - the setting key
    
    Returns:
    
    the value of the setting
  - containsKey
```
public boolean containsKey(String key)
```
    Test if the settings contains a key.
    
    Parameters:
    
    key - the setting key
    
    Returns:
    
    true if the settins contains the key
  - entrySet
```
public Set<Map.Entry<String,String>> entrySet()
```
    Get an entry set of the setting values.
    
    Returns:
    
    an entry set of the settings

Class Settings

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

AOZAN_DEBUG_KEY

AOZAN_ENABLE_KEY

AOZAN_LOG_LEVEL_KEY

AOZAN_LOG_PATH_KEY

AOZAN_VAR_PATH_KEY

AOZAN_CONF_FILE_PATH

BCL_DATA_PATH_KEY

BCL_SPACE_FACTOR_KEY

HISEQ_CRITICAL_MIN_SPACE_KEY

HISEQ_DATA_PATH_KEY

HISEQ_SPACE_FACTOR_KEY

HISEQ_STEP_KEY

HISEQ_WARNING_MIN_SPACE_KEY

BCL2FASTQ_ADAPTER_FASTA_FILE_PATH_KEY

BCL2FASTQ_ADDITIONNAL_ARGUMENTS_KEY

BCL2FASTQ_COMPRESSION_KEY

BCL2FASTQ_COMPRESSION_LEVEL_KEY

BCL2FASTQ_FASTQ_CLUSTER_COUNT_KEY

BCL2FASTQ_MISMATCHES_KEY

BCL2FASTQ_PATH_KEY

SAMPLESHEET_FORMAT_KEY

SAMPLESHEET_PREFIX_KEY

SAMPLESHEET_PATH_KEY

DEMUX_THREADS_KEY

BCL2FASTQ_WITH_FAILED_READS_KEY

SAMPLESHEET_GENERATOR_COMMAND_KEY

BCL2FASTQ_USE_DOCKER_KEY

DEMUX_ARCHIVE_SAMPLESHEETS_KEY

DEMUX_SPACE_FACTOR_KEY

DEMUX_STEP_KEY

DEMUX_USE_HISEQ_OUTPUT_KEY

FASTQ_DATA_PATH_KEY

FASTQ_SPACE_FACTOR_KEY

FIRST_BASE_REPORT_STEP_KEY

RECOMPRESS_STEP_KEY

RECOMPRESS_DELETE_ORIGINAL_FASTQ_KEY

RECOMPRESS_COMPRESSION_LEVEL_KEY

RECOMPRESS_THREADS_KEY

RECOMPRESS_COMPRESSION_KEY

READ_ONLY_OUTPUT_FILES_KEY

INDEX_HTML_TEMPLATE_KEY

INDEX_SEQUENCES_KEY

LOCK_FILE_KEY

MAIL_ERROR_TO_KEY

MAIL_FOOTER_KEY

MAIL_FROM_KEY

MAIL_HEADER_KEY

MAIL_TO_KEY

QC_REPORT_SAVE_RAW_DATA_KEY

QC_REPORT_SAVE_REPORT_DATA_KEY

QC_REPORT_STYLESHEET_KEY

QC_STEP_KEY

REPORTS_DATA_PATH_KEY

REPORTS_URL_KEY

SEND_MAIL_KEY

SYNC_CONTINUOUS_SYNC_KEY

SYNC_CONTINUOUS_SYNC_MIN_AGE_FILES_KEY

SYNC_EXCLUDE_CIF_KEY

SYNC_SPACE_FACTOR_KEY

SYNC_STEP_KEY

TMP_PATH_KEY

DOCKER_URI_KEY

QC_CONF_FASTQC_CONTAMINANT_FILE_KEY

QC_CONF_FASTQC_KMER_SIZE_KEY

QC_CONF_FASTQC_NOGROUP_KEY

QC_CONF_FASTQC_ADAPTER_FILE_KEY

QC_CONF_FASTQC_LIMITS_FILE_KEY

QC_CONF_FASTQC_EXPGROUP_KEY

QC_CONF_FASTQC_CASAVA_KEY

QC_CONF_FASTQC_NOFILTER_KEY

QC_CONF_FASTQC_NANO_KEY

QC_CONF_FASTQC_BLAST_ARGUMENTS_KEY

QC_CONF_FASTQC_BLAST_DB_PATH_KEY

QC_CONF_FASTQC_BLAST_ENABLE_KEY