public class FilterSamReads extends CommandLineProgram
Modifier and Type | Class and Description |
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protected static class |
FilterSamReads.Filter |
Modifier and Type | Field and Description |
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FilterSamReads.Filter |
FILTER |
java.io.File |
INPUT |
java.io.File |
JAVASCRIPT_FILE |
java.io.File |
OUTPUT |
java.io.File |
READ_LIST_FILE |
htsjdk.samtools.SAMFileHeader.SortOrder |
SORT_ORDER |
boolean |
WRITE_READS_FILES |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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FilterSamReads() |
Modifier and Type | Method and Description |
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protected java.lang.String[] |
customCommandLineValidation()
Put any custom command-line validation in an override of this method.
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protected int |
doWork()
Do the work after command line has been parsed.
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static void |
main(java.lang.String[] args)
Stock main method.
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getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="The SAM or BAM file that will be filtered.", optional=false, shortName="I") public java.io.File INPUT
@Option(doc="Filter.", optional=false) public FilterSamReads.Filter FILTER
@Option(doc="Read List File containing reads that will be included or excluded from the OUTPUT SAM or BAM file.", optional=true, shortName="RLF") public java.io.File READ_LIST_FILE
@Option(doc="SortOrder of the OUTPUT SAM or BAM file, otherwise use the SortOrder of the INPUT file.", optional=true, shortName="SO") public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER
@Option(doc="Create .reads files (for debugging purposes)", optional=true) public boolean WRITE_READS_FILES
@Option(doc="SAM or BAM file to write read excluded results to", optional=false, shortName="O") public java.io.File OUTPUT
@Option(shortName="JS", doc="Filters a SAM or BAM file with a javascript expression using the java javascript-engine. The script puts the following variables in the script context: \'record\' a SamRecord ( https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and \'header\' a SAMFileHeader ( https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Last value of the script should be a boolean to tell wether we should accept or reject the record.", optional=true) public java.io.File JAVASCRIPT_FILE
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
protected java.lang.String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram
public static void main(java.lang.String[] args)
args
- main arguments