Package picard.sam
Class BuildBamIndex
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.BuildBamIndex
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@DocumentedFeature public class BuildBamIndex extends CommandLineProgram
Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
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Field Summary
Fields Modifier and Type Field Description String
INPUT
File
OUTPUT
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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 BuildBamIndex()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Main method for the program.-
Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(shortName="I", doc="A BAM file or GA4GH URL to process. Must be sorted in coordinate order.") public String INPUT
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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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Method Detail
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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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