picard.sam

Class SamToFastq

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.SamToFastq

Direct Known Subclasses:

SamToFastqWithTags

@DocumentedFeature
public class SamToFastq
extends CommandLineProgram

Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger FASTQ format. . See MAQ FASTQ specification for details. This tool can be used by way of a pipe to run BWA MEM on unmapped BAM (uBAM) files efficiently.

In the RC mode (default is True), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input sam file will be reverse-complemented prior to writing it to FASTQ in order restore correctly the original read sequence as it was generated by the sequencer.

Usage example:

 java -jar picard.jar SamToFastq \
     I=input.bam \
     FASTQ=output.fastq
 

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	CLIPPING_ACTION
java.lang.String	CLIPPING_ATTRIBUTE
int	CLIPPING_MIN_LENGTH
java.lang.Boolean	COMPRESS_OUTPUTS_PER_RG
java.io.File	FASTQ
boolean	INCLUDE_NON_PF_READS
boolean	INCLUDE_NON_PRIMARY_ALIGNMENTS
java.io.File	INPUT
boolean	INTERLEAVE
java.io.File	OUTPUT_DIR
boolean	OUTPUT_PER_RG
java.lang.Integer	QUALITY
boolean	RE_REVERSE
java.lang.Integer	READ1_MAX_BASES_TO_WRITE
int	READ1_TRIM
java.lang.Integer	READ2_MAX_BASES_TO_WRITE
int	READ2_TRIM
java.lang.String	RG_TAG
java.io.File	SECOND_END_FASTQ
java.io.File	UNPAIRED_FASTQ

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
SamToFastq()

Method Summary

Modifier and Type	Method and Description
protected static void	assertPairedMates(htsjdk.samtools.SAMRecord record1, htsjdk.samtools.SAMRecord record2)
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Do the work after command line has been parsed.
protected java.util.Map<htsjdk.samtools.SAMReadGroupRecord,java.util.List<htsjdk.samtools.fastq.FastqWriter>>	generateAdditionalWriters(java.util.List<htsjdk.samtools.SAMReadGroupRecord> readGroups, htsjdk.samtools.fastq.FastqWriterFactory factory)
protected void	handleAdditionalRecords(htsjdk.samtools.SAMRecord currentRecord, java.util.Map<htsjdk.samtools.SAMReadGroupRecord,java.util.List<htsjdk.samtools.fastq.FastqWriter>> additionalWriters, htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2)
protected void	initializeAdditionalWriters()

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Argument(doc="Input SAM/BAM file to extract reads from",
          shortName="I")
public java.io.File INPUT

FASTQ

@Argument(shortName="F",
          doc="Output FASTQ file (single-end fastq or, if paired, first end of the pair FASTQ).",
          mutex={"OUTPUT_PER_RG","COMPRESS_OUTPUTS_PER_RG","OUTPUT_DIR"})
public java.io.File FASTQ

SECOND_END_FASTQ

@Argument(shortName="F2",
          doc="Output FASTQ file (if paired, second end of the pair FASTQ).",
          optional=true,
          mutex={"OUTPUT_PER_RG","COMPRESS_OUTPUTS_PER_RG"})
public java.io.File SECOND_END_FASTQ

UNPAIRED_FASTQ

@Argument(shortName="FU",
          doc="Output FASTQ file for unpaired reads; may only be provided in paired-FASTQ mode",
          optional=true,
          mutex={"OUTPUT_PER_RG","COMPRESS_OUTPUTS_PER_RG"})
public java.io.File UNPAIRED_FASTQ

OUTPUT_PER_RG

@Argument(shortName="OPRG",
          doc="Output a FASTQ file per read group (two FASTQ files per read group if the group is paired).",
          optional=true,
          mutex={"FASTQ","SECOND_END_FASTQ","UNPAIRED_FASTQ"})
public boolean OUTPUT_PER_RG

COMPRESS_OUTPUTS_PER_RG

@Argument(shortName="GZOPRG",
          doc="Compress output FASTQ files per read group using gzip and append a .gz extension to the file names.",
          mutex={"FASTQ","SECOND_END_FASTQ","UNPAIRED_FASTQ"})
public java.lang.Boolean COMPRESS_OUTPUTS_PER_RG

RG_TAG

@Argument(shortName="RGT",
          doc="The read group tag (PU or ID) to be used to output a FASTQ file per read group.")
public java.lang.String RG_TAG

OUTPUT_DIR

@Argument(shortName="ODIR",
          doc="Directory in which to output the FASTQ file(s).  Used only when OUTPUT_PER_RG is true.",
          optional=true)
public java.io.File OUTPUT_DIR

RE_REVERSE

@Argument(shortName="RC",
          doc="Re-reverse bases and qualities of reads with negative strand flag set before writing them to FASTQ",
          optional=true)
public boolean RE_REVERSE

INTERLEAVE

@Argument(shortName="INTER",
          doc="Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe which end it came from")
public boolean INTERLEAVE

INCLUDE_NON_PF_READS

@Argument(shortName="NON_PF",
          doc="Include non-PF reads from the SAM file into the output FASTQ files. PF means \'passes filtering\'. Reads whose \'not passing quality controls\' flag is set are non-PF reads. See GATK Dictionary for more info.")
public boolean INCLUDE_NON_PF_READS

CLIPPING_ATTRIBUTE

@Argument(shortName="CLIP_ATTR",
          doc="The attribute that stores the position at which the SAM record should be clipped",
          optional=true)
public java.lang.String CLIPPING_ATTRIBUTE

CLIPPING_ACTION

@Argument(shortName="CLIP_ACT",
          doc="The action that should be taken with clipped reads: \'X\' means the reads and qualities should be trimmed at the clipped position; \'N\' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region.",
          optional=true)
public java.lang.String CLIPPING_ACTION

CLIPPING_MIN_LENGTH

@Argument(shortName="CLIP_MIN",
          doc="When performing clipping with the CLIPPING_ATTRIBUTE and CLIPPING_ACTION parameters, ensure that the resulting reads after clipping are at least CLIPPING_MIN_LENGTH bases long. If the original read is shorter than CLIPPING_MIN_LENGTH then the original read length will be maintained.")
public int CLIPPING_MIN_LENGTH

READ1_TRIM

@Argument(shortName="R1_TRIM",
          doc="The number of bases to trim from the beginning of read 1.")
public int READ1_TRIM

READ1_MAX_BASES_TO_WRITE

@Argument(shortName="R1_MAX_BASES",
          doc="The maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written.  If this value is null then all bases left after trimming will be written.",
          optional=true)
public java.lang.Integer READ1_MAX_BASES_TO_WRITE

READ2_TRIM

@Argument(shortName="R2_TRIM",
          doc="The number of bases to trim from the beginning of read 2.")
public int READ2_TRIM

READ2_MAX_BASES_TO_WRITE

@Argument(shortName="R2_MAX_BASES",
          doc="The maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written.  If this value is null then all bases left after trimming will be written.",
          optional=true)
public java.lang.Integer READ2_MAX_BASES_TO_WRITE

QUALITY

@Argument(shortName="Q",
          doc="End-trim reads using the phred/bwa quality trimming algorithm and this quality.",
          optional=true)
public java.lang.Integer QUALITY

INCLUDE_NON_PRIMARY_ALIGNMENTS

@Argument(doc="If true, include non-primary alignments in the output.  Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments.")
public boolean INCLUDE_NON_PRIMARY_ALIGNMENTS

Constructor Detail

SamToFastq

public SamToFastq()

Method Detail

doWork

protected int doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.

initializeAdditionalWriters

protected void initializeAdditionalWriters()

generateAdditionalWriters

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

handleAdditionalRecords

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

assertPairedMates

protected static void assertPairedMates(htsjdk.samtools.SAMRecord record1,
                                        htsjdk.samtools.SAMRecord record2)

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

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 CommandLineProgram

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.