Package picard.sam

Class SamToFastqWithTags

java.lang.Object
picard.cmdline.CommandLineProgram
picard.sam.SamToFastq
picard.sam.SamToFastqWithTags
public class SamToFastqWithTags extends SamToFastq

Extracts read sequences and qualities from the input SAM/BAM file and SAM/BAM tags and writes them into output files in Sanger FASTQ format. See MAQ FASTQ specification for details.

Usage example:

 java -jar picard.jar SamToFastqWithTags
     I=input.bam
     FASTQ=output.fastq
     SEQUENCE_TAG_GROUP="CR"
     QUALITY_TAG_GROUP="CY"
     SEQUENCE_TAG_GROUP="CB,UR"
     QUALITY_TAG_GROUP="CY,UY"

  • Field Details

    • 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 Details

    • SamToFastqWithTags

      public SamToFastqWithTags()

  • Method Details

    • 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.