Package picard.sam
Class BuildBamIndex
java.lang.Object
picard.cmdline.CommandLineProgram
picard.sam.BuildBamIndex
Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
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Field Summary
FieldsFields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, 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
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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INPUT
@Argument(shortName="I", doc="A BAM file or GA4GH URL to process. Must be sorted in coordinate order.") public PicardHtsPath INPUT -
OUTPUT
@Argument(shortName="O", doc="The BAM index file. Defaults to x.bai if INPUT is x.bam, otherwise INPUT.bai.\nIf INPUT is a URL and OUTPUT is unspecified, defaults to a file in the current directory.", optional=true) public File OUTPUT
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Constructor Details
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BuildBamIndex
public BuildBamIndex()
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Method Details
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doWork
protected int doWork()Main method for the program. Checks that all input files are present and readable and that the output file can be written to. Then iterates through all the records generating a BAM Index, then writes the bai file.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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