Package picard.sam
Class SamFormatConverter
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.SamFormatConverter
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@DocumentedFeature public class SamFormatConverter extends CommandLineProgram
Converts a BAM file to human-readable SAM output or vice versa
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Field Summary
Fields Modifier and Type Field Description File
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 SamFormatConverter()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static void
convert(File input, File output, File referenceSequence, Boolean createIndex)
Convert a file from one of sam/bam/cram format to another based on the extension of output.protected int
doWork()
Do the work after command line has been parsed.-
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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Method Detail
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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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convert
public static void convert(File input, File output, File referenceSequence, Boolean createIndex)
Convert a file from one of sam/bam/cram format to another based on the extension of output.- Parameters:
input
- input file in one of sam/bam/cram formatoutput
- output to write converted file to, the conversion is based on the extension of this filenamereferenceSequence
- the reference sequence to use, necessary when reading/writing cramcreateIndex
- whether or not an index should be written alongside the output file
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