picard.util

Class BaitDesigner

java.lang.Object

picard.cmdline.CommandLineProgram

picard.util.BaitDesigner

public class BaitDesigner
extends CommandLineProgram

Designs baits for hybrid selection!

Author:

Tim Fennell

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BaitDesigner.DesignStrategy Set of possible design strategies for bait design.

Field Summary

Fields

Modifier and Type	Field and Description
int	BAIT_OFFSET
int	BAIT_SIZE
java.lang.String	DESIGN_NAME
boolean	DESIGN_ON_TARGET_STRAND
BaitDesigner.DesignStrategy	DESIGN_STRATEGY
boolean	FILL_POOLS
java.lang.String	LEFT_PRIMER
boolean	MERGE_NEARBY_TARGETS
int	MINIMUM_BAITS_PER_TARGET
boolean	OUTPUT_AGILENT_FILES
java.io.File	OUTPUT_DIRECTORY
int	PADDING
int	POOL_SIZE
java.io.File	REFERENCE_SEQUENCE
int	REPEAT_TOLERANCE
java.lang.String	RIGHT_PRIMER
java.io.File	TARGETS

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
BaitDesigner()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Main method that coordinates the checking of inputs, designing of baits and then the writing out of all necessary files.
static int	getMaskedBaseCount(byte[] bases, int from, int until) Returns the total of soft or hard masked bases in the interval of bases.
static void	main(java.lang.String[] args) Stock main method.

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

TARGETS

@Option(shortName="T",
        doc="The file with design parameters and targets")
public java.io.File TARGETS

DESIGN_NAME

@Option(doc="The name of the bait design")
public java.lang.String DESIGN_NAME

REFERENCE_SEQUENCE

@Option(shortName="R",
        doc="The reference sequence fasta file")
public java.io.File REFERENCE_SEQUENCE

LEFT_PRIMER

@Option(doc="The left amplification primer to prepend to all baits for synthesis")
public java.lang.String LEFT_PRIMER

RIGHT_PRIMER

@Option(doc="The right amplification primer to prepend to all baits for synthesis")
public java.lang.String RIGHT_PRIMER

DESIGN_STRATEGY

@Option(doc="The design strategy to use to layout baits across each target")
public BaitDesigner.DesignStrategy DESIGN_STRATEGY

BAIT_SIZE

@Option(doc="The length of each individual bait to design")
public int BAIT_SIZE

MINIMUM_BAITS_PER_TARGET

@Option(doc="The minimum number of baits to design per target.")
public int MINIMUM_BAITS_PER_TARGET

BAIT_OFFSET

@Option(doc="The desired offset between the start of one bait and the start of another bait for the same target.")
public int BAIT_OFFSET

PADDING

@Option(doc="Pad the input targets by this amount when designing baits. Padding is applied on both sides in this amount.")
public int PADDING

REPEAT_TOLERANCE

@Option(doc="Baits that have more than REPEAT_TOLERANCE soft or hard masked bases will not be allowed")
public int REPEAT_TOLERANCE

POOL_SIZE

@Option(doc="The size of pools or arrays for synthesis. If no pool files are desired, can be set to 0.")
public int POOL_SIZE

FILL_POOLS

@Option(doc="If true, fill up the pools with alternating fwd and rc copies of all baits. Equal copies of all baits will always be maintained")
public boolean FILL_POOLS

DESIGN_ON_TARGET_STRAND

@Option(doc="If true design baits on the strand of the target feature, if false always design on the + strand of the genome.")
public boolean DESIGN_ON_TARGET_STRAND

MERGE_NEARBY_TARGETS

@Option(doc="If true merge targets that are \'close enough\' that designing against a merged target would be more efficient.")
public boolean MERGE_NEARBY_TARGETS

OUTPUT_AGILENT_FILES

@Option(doc="If true also output .design.txt files per pool with one line per bait sequence")
public boolean OUTPUT_AGILENT_FILES

OUTPUT_DIRECTORY

@Option(shortName="O",
        optional=true,
        doc="The output directory. If not provided then the DESIGN_NAME will be used as the output directory")
public java.io.File OUTPUT_DIRECTORY

Constructor Detail

BaitDesigner

public BaitDesigner()

Method Detail

getMaskedBaseCount

public static int getMaskedBaseCount(byte[] bases,
                                     int from,
                                     int until)

Returns the total of soft or hard masked bases in the interval of bases.

main

public static void main(java.lang.String[] args)

Stock main method.

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

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 message to be written to the appropriate place.

doWork

protected int doWork()

Main method that coordinates the checking of inputs, designing of baits and then the writing out of all necessary files.

Specified by:

doWork in class CommandLineProgram

Returns: