Package picard.util
Class BaitDesigner
java.lang.Object
picard.cmdline.CommandLineProgram
picard.util.BaitDesigner
Designs baits for hybrid selection!
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic enum
Set of possible design strategies for bait design. -
Field Summary
FieldsModifier and TypeFieldDescriptionint
int
boolean
boolean
boolean
int
boolean
int
int
int
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, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected String[]
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
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Details
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TARGETS
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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 -
RIGHT_PRIMER
@Argument(doc="The right amplification primer to prepend to all baits for synthesis") public String RIGHT_PRIMER -
DESIGN_STRATEGY
@Argument(doc="The design strategy to use to layout baits across each target") public BaitDesigner.DesignStrategy DESIGN_STRATEGY -
BAIT_SIZE
@Argument(doc="The length of each individual bait to design") public int BAIT_SIZE -
MINIMUM_BAITS_PER_TARGET
@Argument(doc="The minimum number of baits to design per target.") public int MINIMUM_BAITS_PER_TARGET -
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 -
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 -
REPEAT_TOLERANCE
@Argument(doc="Baits that have more than REPEAT_TOLERANCE soft or hard masked bases will not be allowed") public int REPEAT_TOLERANCE -
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 -
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 -
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 -
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 -
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 -
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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Constructor Details
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BaitDesigner
public BaitDesigner()
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Method Details
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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. -
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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