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FifoBuffer (Picard)

Acts as a large memory buffer between processes that are connected with unix pipes for the case that one or more processes produces or consumes their input or output in bursts. By inserting a large memory buffer between such processes each process can run at full speed and the bursts can be smoothed out by the memory buffer.

Example

java -jar SamToFastq.jar \ F=my.fastq \ INTERLEAVE=true | java -jar FifoBuffer | bwa mem -t 8 \dev\stdin output.bam

Category Other


Overview

Summary

Acts as a large memory buffer between processes that are connected with unix pipes for the case that one or more processes produces or consumes their input or output in bursts. By inserting a large memory buffer between such processes each process can run at full speed and the bursts can be smoothed out by the memory buffer.

Example

   java -jar SamToFastq.jar \
      F=my.fastq \
      INTERLEAVE=true |
   java -jar FifoBuffer |
   bwa mem -t 8 -Y reference.fasta \dev\stdin output.bam
  

FifoBuffer (Picard) specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--BUFFER_SIZE
536870912 The size of the memory buffer in bytes.
--DEBUG_FREQUENCY
0 How frequently, in seconds, to report debugging statistics. Set to zero for never.
--help
 -h
false display the help message
--IO_SIZE
65536 The size, in bytes, to read/write atomically to the input and output streams.
--NAME
null Name to use for Fifo in debugging statements.
--version
false display the version number for this tool
Optional Common Arguments
--COMPRESSION_LEVEL
5 Compression level for all compressed files created (e.g. BAM and VCF).
--CREATE_INDEX
false Whether to create a BAM index when writing a coordinate-sorted BAM file.
--CREATE_MD5_FILE
false Whether to create an MD5 digest for any BAM or FASTQ files created.
--GA4GH_CLIENT_SECRETS
client_secrets.json Google Genomics API client_secrets.json file path.
--MAX_RECORDS_IN_RAM
500000 When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
--QUIET
true Whether to suppress job-summary info on System.err.
--REFERENCE_SEQUENCE
 -R
null Reference sequence file.
--TMP_DIR
[] One or more directories with space available to be used by this program for temporary storage of working files
--USE_JDK_DEFLATER
 -use_jdk_deflater
false Use the JDK Deflater instead of the Intel Deflater for writing compressed output
--USE_JDK_INFLATER
 -use_jdk_inflater
false Use the JDK Inflater instead of the Intel Inflater for reading compressed input
--VALIDATION_STRINGENCY
STRICT Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
--VERBOSITY
INFO Control verbosity of logging.
Advanced Arguments
--showHidden
false display hidden arguments

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.


--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []


--BUFFER_SIZE / NA

The size of the memory buffer in bytes.

int  536870912  [ [ -∞  ∞ ] ]


--COMPRESSION_LEVEL / NA

Compression level for all compressed files created (e.g. BAM and VCF).

int  5  [ [ -∞  ∞ ] ]


--CREATE_INDEX / NA

Whether to create a BAM index when writing a coordinate-sorted BAM file.

Boolean  false


--CREATE_MD5_FILE / NA

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean  false


--DEBUG_FREQUENCY / NA

How frequently, in seconds, to report debugging statistics. Set to zero for never.

int  0  [ [ -∞  ∞ ] ]


--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json


--help / -h

display the help message

boolean  false


--IO_SIZE / NA

The size, in bytes, to read/write atomically to the input and output streams.

int  65536  [ [ -∞  ∞ ] ]


--MAX_RECORDS_IN_RAM / NA

When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.

Integer  500000  [ [ -∞  ∞ ] ]


--NAME / NA

Name to use for Fifo in debugging statements.

String  null


--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  true


--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--TMP_DIR / NA

One or more directories with space available to be used by this program for temporary storage of working files

List[File]  []


--USE_JDK_DEFLATER / -use_jdk_deflater

Use the JDK Deflater instead of the Intel Deflater for writing compressed output

Boolean  false


--USE_JDK_INFLATER / -use_jdk_inflater

Use the JDK Inflater instead of the Intel Inflater for reading compressed input

Boolean  false


--VALIDATION_STRINGENCY / NA

Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT
LENIENT
SILENT

ValidationStringency  STRICT


--VERBOSITY / NA

Control verbosity of logging.

The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR
WARNING
INFO
DEBUG

LogLevel  INFO


--version / NA

display the version number for this tool

boolean  false


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GATK version 4.1.2.0 built at Tue, 23 Apr 2019 14:55:55 -0400.