Difference between revisions of "LibStatGen: BAM"

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[[Category:C++]]
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[[Category:libStatGen]]
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[[Category:libStatGen BAM]]
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= SAM/BAM File=
 
= SAM/BAM File=
  
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== Reading/Writing SAM/BAM Files ==
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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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The SamFile class allows a user to easily read/write a SAM/BAM file.
 
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This methods found in this class are:
 
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{| class="wikitable" style="width:100%" border="1"
 
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|+ style="font-size:150%"|'''SamFile Class Methods'''
 
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!  width=""|Method Name
 
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!  width=""|Description
 
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|-
 
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| bool OpenForRead(const char* filename)
 
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| Opens the specified file for reading.
 
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Determines if it is a BAM/SAM file by reading the beginning of the file.
 
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Returns true if successfully opened reading, false if not.
 
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|-
 
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| bool OpenForWrite(const char * filename)
 
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| bool: true if successfully opened, false if not.
 
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Opens as BAM file if the specified filename ends in .bam.  Otherwise it is opened as a SAM file.
 
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Returns true if successfully opened for writing, false if not.
 
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|-
 
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| bool ReadHeader(SamFileHeader& header)
 
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| Reads the header section from the file and stores it in the passed in header.
 
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Returns true if successfully read, false if not.
 
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|-
 
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| bool WriteHeader(const SamFileHeader& header)
 
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| Writes the specified header into the file.
 
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Returns true if successfully written, false if not.
 
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|- 
 
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| bool ReadRecord(SamFileHeader& header, SamRecord& record)
 
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| Reads the next record from the file and stores it in the passed in record.
 
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Returns true if successfully read, false if not.
 
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|-
 
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| bool WriteRecord(SamFileHeader& header, SamRecord& record)
 
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| Writes the specified record into the file.
 
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Returns true if successfully written, false if not.
 
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|}
 
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=== Usage Example ===
 
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The following example reads in a sam/bam file and writes it out as a sam/bam file.  The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file.  The file format of the output sam/bam file is determined by the SamFile class based on the extension of the output file.  A ".bam" extension indicates a BAM file.  All other extensions indicate SAM files.
 
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<pre>
 
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int main(int argc, char ** argv)
 
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{
 
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  if(argc != 3)
 
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  {
 
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      printf("./bam <inputFile> <outputFile.sam/bam>\n");
 
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      exit(-1);
 
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  }
 
  
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[[BAM Review Action Items|Old BAM Review Action Items]]
  
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  SamFile samIn;
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== Read & Write BAM/SAM Library Software ==
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  samIn.OpenForRead(argv[1]);
 
  
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  SamFile samOut;
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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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  samOut.OpenForWrite(argv[2]);
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The library is found in statgen/lib/bam.
  
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  // Read the sam header.
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=== BAM/SAM Classes ===
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  SamFileHeader samHeader;
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{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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  samIn.ReadHeader(samHeader);
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|-style="background: #f2f2f2; text-align: center;"
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! Class Name !!  Description
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  samOut.WriteHeader(samHeader);
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|-
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| <code>[[C++ Class: SamFile|SamFile]]</code>
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  // Read the first sam record.
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| Class used for reading/writing SAM/BAM files and their headers and records.
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  SamRecord samRecord;
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|-
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| <code>[[C++ Class: SamFileHeader|SamFileHeader]]</code>
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  // Keep reading records until it fails.
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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.
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  int recordCount = 0;
 
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  while (samIn.ReadRecord(samHeader, samRecord) == true)
 
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  {
 
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      recordCount++;
 
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      samOut.WriteRecord(samHeader, samRecord);
 
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  }
 
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  printf("RecordCount = %d\n", recordCount);
 
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}
 
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</pre>
 
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== Setting fields in a SAM/BAM Record ==
 
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The SamRecord class contains accessors to set the fields of a SAM/BAM record.  They are used for creating a record that is not read from a SAM/BAM file.  By using these set methods to setup the record, they can be pulled back out using the get accessors or the record can be later written as either a SAM/BAM record.
 
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This methods found in the SamRecord class for setting fields are:
 
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{| class="wikitable" style="width:100%" border="1"
 
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|+ style="font-size:150%"|'''SamFile Class Methods'''
 
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!  width=""|Method Name
 
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! width=""|Description
 
 
|-
 
|-
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| bool setReadName(const char* readName)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecord]</code>
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| Sets QNAME to the passed in name.
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| Class used for storing the tag/value pairs within a given header line.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool setFlag(int flag)
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| <code>[[C++ Class: SamRecord|SamRecord]]</code>
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| Sets the bitwise FLAG to the passed in value.
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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.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool setReferenceID(int referenceID)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamStatus.html SamStatus]</code>
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| Sets the reference sequence id. The reference name is not currently stored. A map to the header needs to be done to get this (which is done when writing a SAM file). THIS is an opportunity for improvement.
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| Status value used by the BAM classes for returning the status of the operations.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool set1BasedPosition(int position)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamValidator.html SamValidator]</code>
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| Sets the leftmost position. The value passed in is 1-based (SAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
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| Validates a SAM/BAM Record.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool set0BasedPosition(int position)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamValidationError.html SamValidationError]</code>
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| Sets the leftmost position. The value passed in is 0-based (BAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
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| Validation Error Information for a SamRecord.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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|bool setMapQuality(int mapQuality)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamValidationErrors.html SamValidationErrors]</code>
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| Sets the mapping quality.
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| Container for ValidationErrors.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool setCigar(const char* cigar)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPileup.html Pileup]</code>
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| Sets the cigar string to the passed in CIGAR. This is a SAM formatted CIGAR string. Internal processing handles switching between SAM/BAM formats when read/written.
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| Template for doing pileups.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool setMateReferenceID(int mateReferenceID)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPileupElement.html PileupElement]</code>
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| Sets the mate reference sequence id.  The mate reference name is not currently stored.  A map to the header needs to be done to get this (which is done when writing a SAM file).  THIS is an opportunity for improvement.
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| Base class that can be used for the elements stored in a Pileup.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool set1BasedMatePosition(int matePosition)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classErrorHandler.html ErrorHandler]</code>
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| Sets the leftmost mate position. The value passed in is 1-based (SAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
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| Class for handling errors based on the error handling type.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool set0BasedMatePosition(int matePosition)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPosList.html PosList]</code>
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| Sets the leftmost mate position. The value passed in is 0-based (BAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
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| Store refID/position, but does not store values < 0.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool setInsertSize(int insertSize)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFilter.html SamFilter]</code>
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| Sets the inferred insert size.
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| Class for filtering a SAM/BAM record.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool setSequence(const char* seq)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFlag.html SamFlag]</code>
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| Sets the sequence string to the passed in string.  This is a SAM formatted sequence string.  Internal processing handles switching between SAM/BAM formats when read/written.
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| Class for getting information from a SAM/BAM flag.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool setQuality(const char* quality)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamReferenceInfo.html SamReferenceInfo]</code>
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| Sets the quality string to the passed in string. This is a SAM formatted quality string. Internal processing handles switching between SAM/BAM formats when read/written.
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| Class for tracking the reference information mapping between the reference ids and the reference names.
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Returns true if successfully set, false if not.
 
 
|-
 
|-
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| bool addTag(const char* tag, char vtype, const char* value)
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamTags.html SamTags]</code>
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| Adds a tag to the record with the specified tag, vtype, and value.  Vtype can be SAM/BAM vtype.  Internal processing handles switching between SAM/BAM vtypes when read/written.
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| Class for parsing/creating/operating on SAM/BAM record tags.
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Returns true if successfully set, false if not.
 
 
|}
 
|}
  
 +
== FAQs ==
 +
[[SAM/BAM Classes FAQs]]
 +
 +
== Usage Examples ==
 +
[[Sam Library Usage Examples]]
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 +
== Programs ==
  
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== Retrieving fields from a SAM/BAM Record ==
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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.
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The SamRecord class contains accessors to access the fields of a SAM/BAM record.  They assume that the class has already been populated, either by using the set commands or by calling SamFile::ReadRecord.
 

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"