Field Detail

• SEQUENCE_TAG_GROUP

  @Argument(shortName="STG",
            doc="List of comma separated tag values to extract from Input SAM/BAM to be used as read sequence",
            minElements=1)
  public List<String> SEQUENCE_TAG_GROUP

• QUALITY_TAG_GROUP

  @Argument(shortName="QTG",
            doc="List of comma separated tag values to extract from Input SAM/BAM to be used as read qualities",
            optional=true)
  public List<String> QUALITY_TAG_GROUP

• TAG_GROUP_SEPERATOR

  @Argument(shortName="SEP",
            doc="List of any sequences (e.g. \'AACCTG`) to put in between each comma separated list of sequence tags in each SEQUENCE_TAG_GROUP (STG)",
            optional=true)
  public List<String> TAG_GROUP_SEPERATOR

• COMPRESS_OUTPUTS_PER_TAG_GROUP

  @Argument(shortName="GZOPTG",
            doc="Compress output FASTQ files per Tag grouping using gzip and append a .gz extension to the file names.")
  public Boolean COMPRESS_OUTPUTS_PER_TAG_GROUP

Constructor Detail

• SamToFastqWithTags

  public SamToFastqWithTags()

Method Detail

• initializeAdditionalWriters

  protected void initializeAdditionalWriters()

  Overrides:

  initializeAdditionalWriters in class SamToFastq

• handleAdditionalRecords

  protected void handleAdditionalRecords​(htsjdk.samtools.SAMRecord currentRecord,
                                         Map<htsjdk.samtools.SAMReadGroupRecord,List<htsjdk.samtools.fastq.FastqWriter>> tagWriters,
                                         htsjdk.samtools.SAMRecord read1,
                                         htsjdk.samtools.SAMRecord read2)

  Overrides:

  handleAdditionalRecords in class SamToFastq

• generateAdditionalWriters

  protected Map<htsjdk.samtools.SAMReadGroupRecord,List<htsjdk.samtools.fastq.FastqWriter>> generateAdditionalWriters​(List<htsjdk.samtools.SAMReadGroupRecord> readGroups,
                                                                                                                      htsjdk.samtools.fastq.FastqWriterFactory factory)

  Overrides:

  generateAdditionalWriters in class SamToFastq

• customCommandLineValidation

  protected String[] customCommandLineValidation()

  Description copied from class: SamToFastq
  Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

  Overrides:

  customCommandLineValidation in class SamToFastq

  Returns:

  null if command line is valid. If command line is invalid, returns an array of error messages to be written to the appropriate place.