Difference between revisions of "LibStatGen: BAM"

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[[Category:Software|libbam]]
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[[Category:C++]]
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[[Category:libStatGen]]
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[[Category:libStatGen BAM]]
  
 
= SAM/BAM File=
 
= SAM/BAM File=
  
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See [[C++ Library: libbam Change Log]] for a list of the most recent updates to the library.
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See the github history: https://github.com/statgen/libStatGen/commits/master/bam for a list of the most recent updates to the BAM classes.
  
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== Read & Write BAM/SAM Library ==
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[[BAM Review Action Items|Old BAM Review Action Items]]
  
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The software reads the beginning of files opened for reading to determine if it is SAM/BAM.  To determine the format (SAM/BAM) of files open for writing, the software checks the output file's extension.  If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file.
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== Read & Write BAM/SAM Library Software ==
  
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The library is found in pipeline/bam, and is called libbam.a.
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The software reads the beginning of files opened for reading to determine if it is SAM/BAM.  To determine the format (SAM/BAM) of files open for writing, the software checks the output file's extension.  If the extension is "bam" it writes a BAM file, otherwise it writes a SAM file.
  
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This library is dependent on two other libraries:
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The library is found in statgen/lib/bam.
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# [[C++ Library: libcsg|libcsg/libcsg.a]]
 
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# thirdParty/samtools/libbam.a
 
  
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Be sure to include them all in the proper order:
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=== BAM/SAM Classes ===
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<path to base pipeline directory>/libbam.a <path to base pipeline directory>/libcsg/libcsg.a <path to base pipeline directory>/thirdParty/samtools/libbam.a
 
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=== Classes in the BAM/SAM Library ===
 
 
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 
|-style="background: #f2f2f2; text-align: center;"
 
|-style="background: #f2f2f2; text-align: center;"
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| Class used for storing the header.  Allows access for getting and setting header values when both reading & writing SAM/BAM files.
 
| Class used for storing the header.  Allows access for getting and setting header values when both reading & writing SAM/BAM files.
 
|-
 
|-
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| <code>[[C++ Class: SamHeaderRecord|SamHeaderRecord]]</code>
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecord]</code>
 
| Class used for storing the tag/value pairs within a given header line.
 
| Class used for storing the tag/value pairs within a given header line.
 
|-
 
|-
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| Class used for storing a SAM/BAM Record.  Allows access for getting and setting record values when both reading & writing SAM/BAM files.
 
| Class used for storing a SAM/BAM Record.  Allows access for getting and setting record values when both reading & writing SAM/BAM files.
 
|-
 
|-
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| <code>[[C++ Class: SamStatus|SamStatus]]</code>
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamStatus.html SamStatus]</code>
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| Status value used by the libbam classes for returning the status of the operations.
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| Status value used by the BAM classes for returning the status of the operations.
 
|-
 
|-
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| <code>[[C++ Class: SamValidator|SamValidator]]</code>
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamValidator.html SamValidator]</code>
 
| Validates a SAM/BAM Record.
 
| Validates a SAM/BAM Record.
 
|-
 
|-
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| <code>[[C++ Class: SamValidationError|SamValidationError]]</code>
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamValidationError.html SamValidationError]</code>
 
| Validation Error Information for a SamRecord.
 
| Validation Error Information for a SamRecord.
 
|-
 
|-
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| <code>[[C++ Class: SamValidationErrors|SamValidationErrors]]</code>
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamValidationErrors.html SamValidationErrors]</code>
 
| Container for ValidationErrors.
 
| Container for ValidationErrors.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPileup.html Pileup]</code>
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| Template for doing pileups.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPileupElement.html PileupElement]</code>
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| Base class that can be used for the elements stored in a Pileup.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classErrorHandler.html ErrorHandler]</code>
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| Class for handling errors based on the error handling type.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPosList.html PosList]</code>
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| Store refID/position, but does not store values < 0.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFilter.html SamFilter]</code>
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| Class for filtering a SAM/BAM record.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFlag.html SamFlag]</code>
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| Class for getting information from a SAM/BAM flag.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamReferenceInfo.html SamReferenceInfo]</code>
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| Class for tracking the reference information mapping between the reference ids and the reference names.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamTags.html SamTags]</code>
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| Class for parsing/creating/operating on SAM/BAM record tags.
 
|}
 
|}
  
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== Executable ==
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== FAQs ==
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An executable that converts between SAM and BAM formats and that can validate SAM/BAM Records has been developed: [[C++ Executable: bam|bam]]
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[[SAM/BAM Classes FAQs]]
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== Usage Examples ==
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[[Sam Library Usage Examples]]
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== Programs ==
  
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== Suggested Improvements/Features ==
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BamUtil contains a set of programs that uses this library to operate on SAM & BAM files.  It includes tools for converting between SAM & BAM and validating the files.  See [[BamUtil]] for more information and a description of all the tools.

Latest revision as of 10:55, 2 February 2017


SAM/BAM File

See the github history: https://github.com/statgen/libStatGen/commits/master/bam for a list of the most recent updates to the BAM classes.

Old BAM Review Action Items

Read & Write BAM/SAM Library Software

The software reads the beginning of files opened for reading to determine if it is SAM/BAM. To determine the format (SAM/BAM) of files open for writing, the software checks the output file's extension. If the extension is "bam" it writes a BAM file, otherwise it writes a SAM file.

The library is found in statgen/lib/bam.

BAM/SAM Classes

Class Name Description
SamFile Class used for reading/writing SAM/BAM files and their headers and records.
SamFileHeader Class used for storing the header. Allows access for getting and setting header values when both reading & writing SAM/BAM files.
SamHeaderRecord Class used for storing the tag/value pairs within a given header line.
SamRecord Class used for storing a SAM/BAM Record. Allows access for getting and setting record values when both reading & writing SAM/BAM files.
SamStatus Status value used by the BAM classes for returning the status of the operations.
SamValidator Validates a SAM/BAM Record.
SamValidationError Validation Error Information for a SamRecord.
SamValidationErrors Container for ValidationErrors.
Pileup Template for doing pileups.
PileupElement Base class that can be used for the elements stored in a Pileup.
ErrorHandler Class for handling errors based on the error handling type.
PosList Store refID/position, but does not store values < 0.
SamFilter Class for filtering a SAM/BAM record.
SamFlag Class for getting information from a SAM/BAM flag.
SamReferenceInfo Class for tracking the reference information mapping between the reference ids and the reference names.
SamTags Class for parsing/creating/operating on SAM/BAM record tags.

FAQs

SAM/BAM Classes FAQs

Usage Examples

Sam Library Usage Examples


Programs

BamUtil contains a set of programs that uses this library to operate on SAM & BAM files. It includes tools for converting between SAM & BAM and validating the files. See BamUtil for more information and a description of all the tools.

Retrieved from "http://genome.sph.umich.edu/w/index.php?title=LibStatGen:_BAM&oldid=14600"