@DocumentedFeature public class BamToBfq extends CommandLineProgram
The BFQ format is the input format to some tools like Maq aligner.
A single BAM file to convert
.One or two FASTQ files depending on whether the BAM file contains single- or
paired-end sequencing data. You must indicate the output directory that will contain these files (ANALYSIS_DIR)
and the output file name prefix (OUTPUT_FILE_PREFIX).
java -jar picard.jar BamToBfq \
I=input.bam \
ANALYSIS_DIR=output_dir \
OUTPUT_FILE_PREFIX=output_name \
PAIRED_RUN=false
| Modifier and Type | Field | Description |
|---|---|---|
File |
ANALYSIS_DIR |
|
Integer |
BASES_TO_WRITE |
|
boolean |
CLIP_ADAPTERS |
|
String |
FLOWCELL_BARCODE |
|
Boolean |
INCLUDE_NON_PF_READS |
|
File |
INPUT |
|
Integer |
LANE |
|
String |
OUTPUT_FILE_PREFIX |
|
Boolean |
PAIRED_RUN |
|
Integer |
READ_CHUNK_SIZE |
|
String |
READ_NAME_PREFIX |
|
Integer |
READS_TO_ALIGN |
|
String |
RUN_BARCODE |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY| Constructor | Description |
|---|---|
BamToBfq() |
| Modifier and Type | Method | Description |
|---|---|---|
protected 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.
|
static void |
main(String[] argv) |
getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(doc="The BAM file to parse.",
shortName="I")
public File INPUT
@Argument(doc="The analysis directory for the binary output file. ") public File ANALYSIS_DIR
@Argument(doc="Flowcell barcode (e.g. 30PYMAAXX). ",
shortName="F",
mutex="OUTPUT_FILE_PREFIX")
public String FLOWCELL_BARCODE
@Argument(doc="Lane number. ",
shortName="L",
optional=true,
mutex="OUTPUT_FILE_PREFIX")
public Integer LANE
@Argument(doc="Prefix for all output files",
mutex={"FLOWCELL_BARCODE","LANE"})
public String OUTPUT_FILE_PREFIX
@Argument(doc="Number of reads to align (null = all).",
shortName="NUM",
optional=true)
public Integer READS_TO_ALIGN
@Argument(doc="Number of reads to break into individual groups for alignment",
shortName="CHUNK")
public Integer READ_CHUNK_SIZE
@Argument(doc="Whether this is a paired-end run. ",
shortName="PE")
public Boolean PAIRED_RUN
@Argument(doc="Deprecated option; use READ_NAME_PREFIX instead",
mutex="READ_NAME_PREFIX",
shortName="RB",
optional=true)
public String RUN_BARCODE
@Argument(doc="Prefix to be stripped off the beginning of all read names (to make them short enough to run in Maq)",
optional=true)
public String READ_NAME_PREFIX
@Argument(doc="Whether to include non-PF reads",
shortName="NONPF",
optional=true)
public Boolean INCLUDE_NON_PF_READS
@Argument(doc="Whether to clip adapters from the reads") public boolean CLIP_ADAPTERS
@Argument(doc="The number of bases from each read to write to the bfq file. If this is non-null, then only the first BASES_TO_WRITE bases from each read will be written.",
optional=true)
public Integer BASES_TO_WRITE
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgrampublic static void main(String[] argv)
protected String[] customCommandLineValidation()
CommandLineProgramcustomCommandLineValidation in class CommandLineProgram