ViewSam (picard 2.18.2 API)

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 Description

static class ViewSam.AlignmentStatus

static class ViewSam.PfStatus

Nested Classes
Modifier and Type	Class	Description
`static class`	`ViewSam.AlignmentStatus`
`static class`	`ViewSam.PfStatus`

Field Summary

Fields
Modifier and Type	Field	Description
`ViewSam.AlignmentStatus`	`ALIGNMENT_STATUS`
`boolean`	`HEADER_ONLY`
`String`	`INPUT`
`File`	`INTERVAL_LIST`
`ViewSam.PfStatus`	`PF_STATUS`
`boolean`	`RECORDS_ONLY`
`String`	`USAGE`

Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors
Constructor Description

ViewSam()

Constructors
Constructor	Description
`ViewSam()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected 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.
`static void`	`main(String[] args)`

Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, 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 String USAGE
```
  - INPUT
```
@Argument(shortName="I",
          doc="The SAM or BAM file or GA4GH url to view.")
public 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 File INTERVAL_LIST
```
- Constructor Detail
  - ViewSam
```
public ViewSam()
```
- Method Detail
  - main
```
public static void main(String[] args)
```
  - 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 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.

Class ViewSam

Inputs

Usage example:

Nested Class Summary

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

USAGE

INPUT

ALIGNMENT_STATUS

PF_STATUS

HEADER_ONLY

RECORDS_ONLY

INTERVAL_LIST

Constructor Detail

ViewSam

Method Detail

main

doWork

customCommandLineValidation