Package picard.util
Class BaitDesigner
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.util.BaitDesigner
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@DocumentedFeature public class BaitDesigner extends CommandLineProgram
Designs baits for hybrid selection!
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
BaitDesigner.DesignStrategy
Set of possible design strategies for bait design.
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Field Summary
Fields Modifier and Type Field Description int
BAIT_OFFSET
int
BAIT_SIZE
String
DESIGN_NAME
boolean
DESIGN_ON_TARGET_STRAND
BaitDesigner.DesignStrategy
DESIGN_STRATEGY
boolean
FILL_POOLS
String
LEFT_PRIMER
boolean
MERGE_NEARBY_TARGETS
int
MINIMUM_BAITS_PER_TARGET
boolean
OUTPUT_AGILENT_FILES
File
OUTPUT_DIRECTORY
int
PADDING
int
POOL_SIZE
int
REPEAT_TOLERANCE
String
RIGHT_PRIMER
File
TARGETS
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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
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Constructor Summary
Constructors Constructor Description BaitDesigner()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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 int
getMaskedBaseCount(byte[] bases, int from, int until)
Returns the total of soft or hard masked bases in the interval of bases.protected boolean
requiresReference()
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Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Detail
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TARGETS
@Argument(shortName="T", doc="The file with design parameters and targets") public File TARGETS
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DESIGN_NAME
@Argument(doc="The name of the bait design") public String DESIGN_NAME
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LEFT_PRIMER
@Argument(doc="The left amplification primer to prepend to all baits for synthesis") public String LEFT_PRIMER
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RIGHT_PRIMER
@Argument(doc="The right amplification primer to prepend to all baits for synthesis") public String RIGHT_PRIMER
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DESIGN_STRATEGY
@Argument(doc="The design strategy to use to layout baits across each target") public BaitDesigner.DesignStrategy DESIGN_STRATEGY
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BAIT_SIZE
@Argument(doc="The length of each individual bait to design") public int BAIT_SIZE
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MINIMUM_BAITS_PER_TARGET
@Argument(doc="The minimum number of baits to design per target.") public int MINIMUM_BAITS_PER_TARGET
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BAIT_OFFSET
@Argument(doc="The desired offset between the start of one bait and the start of another bait for the same target.") public int BAIT_OFFSET
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PADDING
@Argument(doc="Pad the input targets by this amount when designing baits. Padding is applied on both sides in this amount.") public int PADDING
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REPEAT_TOLERANCE
@Argument(doc="Baits that have more than REPEAT_TOLERANCE soft or hard masked bases will not be allowed") public int REPEAT_TOLERANCE
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POOL_SIZE
@Argument(doc="The size of pools or arrays for synthesis. If no pool files are desired, can be set to 0.") public int POOL_SIZE
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FILL_POOLS
@Argument(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
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DESIGN_ON_TARGET_STRAND
@Argument(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
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MERGE_NEARBY_TARGETS
@Argument(doc="If true merge targets that are \'close enough\' that designing against a merged target would be more efficient.") public boolean MERGE_NEARBY_TARGETS
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OUTPUT_AGILENT_FILES
@Argument(doc="If true also output .design.txt files per pool with one line per bait sequence") public boolean OUTPUT_AGILENT_FILES
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OUTPUT_DIRECTORY
@Argument(shortName="O", optional=true, doc="The output directory. If not provided then the DESIGN_NAME will be used as the output directory") public File OUTPUT_DIRECTORY
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Method Detail
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requiresReference
protected boolean requiresReference()
- Overrides:
requiresReference
in classCommandLineProgram
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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.
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customCommandLineValidation
protected 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 classCommandLineProgram
- 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.
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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 classCommandLineProgram
- Returns:
- program exit status.
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