Package picard.sam
Class SamFormatConverter
java.lang.Object
picard.cmdline.CommandLineProgram
picard.sam.SamFormatConverter
Converts a BAM file to human-readable SAM output or vice versa
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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
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OUTPUT
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Constructor Details
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SamFormatConverter
public SamFormatConverter()
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Method Details
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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
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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