picard.sam

Class ViewSam

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.ViewSam

@DocumentedFeature
public class ViewSam
extends CommandLineProgram

Prints a SAM or BAM file to the screen.

Very simple command that just reads a SAM or BAM file and writes out the header and each record to standard out. When an (optional) intervals file is specified, only records overlapping those intervals will be output.

All reads, just the aligned reads, or just the unaligned reads can be printed out by setting AlignmentStatus accordingly. The SAM or BAM header can be printed out separately using HEADER_ONLY. Only the alignment records can be printed using RECORDS_ONLY. However, HEADER_ONLY and RECORDS_ONLY cannot both be specified at one time.

Inputs

• A SAM or BAM file to be viewed
• Optional arguments specifying which reads or records need to be viewed

Usage example:

     java -jar picard.jar ViewSam \
          I=input_reads.bam \
          HEADER_ONLY=true
 

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ViewSam.AlignmentStatus
static class	ViewSam.PfStatus

Field Summary

Fields

Modifier and Type	Field and Description
ViewSam.AlignmentStatus	ALIGNMENT_STATUS
boolean	HEADER_ONLY
java.lang.String	INPUT
java.io.File	INTERVAL_LIST
ViewSam.PfStatus	PF_STATUS
boolean	RECORDS_ONLY
java.lang.String	USAGE

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

Constructor Summary

Constructors

Constructor and Description
ViewSam()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

USAGE

public final java.lang.String USAGE

INPUT

@Argument(shortName="I",
          doc="The SAM or BAM file or GA4GH url to view.")
public java.lang.String INPUT

ALIGNMENT_STATUS

@Argument(doc="Print out all reads, just the aligned reads or just the unaligned reads.")
public ViewSam.AlignmentStatus ALIGNMENT_STATUS

PF_STATUS

@Argument(doc="Print out all reads, just the PF reads or just the non-PF reads.")
public ViewSam.PfStatus PF_STATUS

HEADER_ONLY

@Argument(doc="Print the SAM header only.",
          optional=true)
public boolean HEADER_ONLY

RECORDS_ONLY

@Argument(doc="Print the alignment records only.",
          optional=true)
public boolean RECORDS_ONLY

INTERVAL_LIST

@Argument(doc="An intervals file used to restrict what records are output.",
          optional=true)
public java.io.File INTERVAL_LIST

Constructor Detail

ViewSam

public ViewSam()

Method Detail

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 class CommandLineProgram

Returns:

program exit status.

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.