Package picard.sam
Class BamIndexStats
- java.lang.Object
-
- picard.cmdline.CommandLineProgram
-
- picard.sam.BamIndexStats
-
@DocumentedFeature public class BamIndexStats extends CommandLineProgram
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.
-
-
Field Summary
Fields Modifier and Type Field Description File
INPUT
-
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, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
-
-
Constructor Summary
Constructors Constructor Description BamIndexStats()
-
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
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
-
-
-
Field Detail
-
INPUT
@Argument(shortName="I", doc="A BAM file to process.") public File INPUT
-
-
Method Detail
-
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.
-
-