Package picard.sam
Class BamIndexStats
java.lang.Object
picard.cmdline.CommandLineProgram
picard.sam.BamIndexStats
Command line program to print statistics from BAM index (.bai) file
Statistics include count of aligned and unaligned reads for each reference sequence
and a count of all records with no start coordinate.
Similar to the 'samtools idxstats' command.
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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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Constructor Details
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BamIndexStats
public BamIndexStats()
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Method Details
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doWork
protected int doWork()Main method for the program. Checks that input file is present and readable, then iterates through the index printing meta data to stdout.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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