C++ Class: SamRecord

Setting fields in a SAM/BAM Record

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. The methods found in the SamRecord class for setting fields are:

Method Name	Description
void SamRecord::resetRecord()	Resets the record to be an empty record. This is not necessary when you are reading a Sam/Bam file, but if you are setting fields, it is a good idea to clean out a record before reusing it. Clearing it allows you to not have to set any empty fields.
bool SamRecord::setReadName(const char* readName)	Sets QNAME to the passed in name. Returns true if successfully set, false if not.
bool SamRecord::setFlag(int16_t flag)	Sets the bitwise FLAG to the passed in value. Returns true if successfully set, false if not.
bool SamRecord::setReferenceName(SamFileHeader& header, const char* referenceName)	Sets the reference sequence name. The reference id is calculated using the header. Returns true if successfully set, false if not.
bool SamRecord::set1BasedPosition(int32_t position)	Sets the leftmost position. The value passed in is 1-based (SAM formatted). Internal processing handles switching between SAM/BAM formats when read/written. Returns true if successfully set, false if not.
bool SamRecord::set0BasedPosition(int32_t position)	Sets the leftmost position. The value passed in is 0-based (BAM formatted). Internal processing handles switching between SAM/BAM formats when read/written. Returns true if successfully set, false if not.
bool SamRecord::setMapQuality(int8_t mapQuality)	Sets the mapping quality. Returns true if successfully set, false if not.
bool SamRecord::setCigar(const char* cigar)	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. Returns true if successfully set, false if not.
bool SamRecord::setMateReferenceName(SamFileHeader& header, const char* referenceName)	Sets the mate reference sequence name. The mate reference id is calculated using the header. Returns true if successfully set, false if not.
bool SamRecord::set1BasedMatePosition(int32_t matePosition)	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. Returns true if successfully set, false if not.
bool SamRecord::set0BasedMatePosition(int32_t matePosition)	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. Returns true if successfully set, false if not.
bool SamRecord::setInsertSize(int32_t insertSize)	Sets the inferred insert size. Returns true if successfully set, false if not.
bool SamRecord::setSequence(const char* seq)	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. Returns true if successfully set, false if not.
bool SamRecord::setQuality(const char* quality)	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. Returns true if successfully set, false if not.
bool SamRecord::addTag(const char* tag, char vtype, const char* value)	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. Returns true if successfully set, false if not.

When set, SAM fields are validated against: SAM Validation Criteria

Retrieving fields from a SAM/BAM Record

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. Not all of the values that can be retrieved using these get accessors have set methods. That is because they are internally calculated values if they were not read from a file.

The methods found in the SamRecord class for setting fields are:

Method Name	Description
bool SamRecord::isValid(SamFileHeader& header)	Returns true if the record is valid. This performs validation steps. TODO: the method exists, but it does not yet perform any checks, so just returns true.
int32_t SamRecord::getBlockSize()	Returns the BAM block size of the record.
const char* SamRecord::getReferenceName(SamFileHeader& header)	Returns the reference sequence name (SAM format).
int32_t SamRecord::getReferenceID()	Returns the reference sequence ID (BAM format).
int32_t SamRecord::get1BasedPosition()	Returns the 1-based (SAM formatted) leftmost position.
int32_t SamRecord::get0BasedPosition()	Returns the 0-based (BAM formatted) leftmost position.
int8_t SamRecord::getReadNameLength()	Returns the length of the ReadName (QNAME).
int8_t SamRecord::getMapQuality()	Returns the map quality.
int16_t SamRecord::getBin()	Returns the BAM bin for the record.
int16_t SamRecord::getCigarLength()	Returns the length of the CIGAR in BAM format.
int16_t SamRecord::getFlag()	Returns the flag.
int32_t SamRecord::getReadLength()	Returns the length of the read.
const char* SamRecord::getMateReferenceName(SamFileHeader& header)	Returns the mate reference sequence name (SAM format). Returns the mate reference sequence name even if it is the same as the reference sequence name.
const char* SamRecord::getMateReferenceNameOrEqual(SamFileHeader& header)	Returns the mate reference sequence name (SAM format). Returns the mate reference sequence name, unless it is the same as the reference sequence name, then an "=" is returned..
int32_t SamRecord::getMateReferenceID()	Returns the mate reference sequence id (BAM format).
int32_t SamRecord::get1BasedMatePosition()	Returns the 1-based (SAM formatted) mate leftmost position.
int32_t SamRecord::get0BasedMatePosition()	Returns the 0-based (BAM formatted) mate leftmost position.
int32_t SamRecord::getInsertSize()	Returns the insert size.
int32_t SamRecord::get0BasedAlignmentEnd()	Returns the 0-based inclusive right-most position of the clipped sequence.
int32_t SamRecord::get1BasedAlignmentEnd()	Returns the 1-based inclusive right-most position of the clipped sequence.
int32_t SamRecord::get0BasedUnclippedStart()	Returns the 0-based inclusive left-most position adjusted for clipped bases.
int32_t SamRecord::get1BasedUnclippedStart()	Returns the 1-based inclusive left-most position adjusted for clipped bases.
int32_t SamRecord::get0BasedUnclippedEnd()	Returns the 0-based inclusive right-most position adjusted for clipped bases.
int32_t SamRecord::get1BasedUnclippedEnd()	Returns the 1-based inclusive right-most position adjusted for clipped bases.
const char* SamRecord::getReadName()	Returns the SAM formatted Read Name (QNAME).
const char* SamRecord::getCigar()	Returns the SAM formatted CIGAR string.
const char* SamRecord::getSequence()	Returns the SAM formatted Sequence string.
const char* SamRecord::getQuality()	Returns the SAM formatted Quality string.
bool SamRecord::getNextSamTag(char* tag, char& vtype, void** value)	Returns true if a tag was read, false if there are no more tags. For a true return value, tag is sent to the tag of the tag, vtype is set to the vtype of the tag, and value is a pointer to the value of the tag. You will then need to use a switch to cast value to int, double, char, or String.
bool SamRecord::isIntegerType(char vtype)	Returns true if the passed in vtype is of integer ('c', 'C', 's', 'S', 'i', 'I') type.
bool SamRecord::isDoubleType(char vtype)	Returns true if the passed in vtype is of double ('f') type.
bool SamRecord::isCharType(char vtype)	Returns true if the passed in vtype is of char ('A') type.
bool SamRecord::isStringType(char vtype)	Returns true if the passed in vtype is of String ('Z') type.

Example of using getNextSamTag:

   // record is a previously setup SamRecord.
   String recordString = "";
   char tag[3];
   char vtype;
   void* value;

   // While there are more tags, write them to the recordString.
   while(record.getNextSamTag(tag, vtype, &value) != false)
   {
      recordString += "\t";
      recordString += tag;
      recordString += ":"; 
      recordString += vtype;
      recordString += ":";
      if(record.isIntegerType(vtype))
      {
         recordString += (int)*(int*)value;
      }
      else if(record.isDoubleType(vtype))
      {
         recordString += (double)*(double*)value;
      }
      else if(record.isCharType(vtype))
      {
         recordString += (char)*(char*)value;
      }
      else
      {
         // String type.
         recordString += (String)*(String*)value;
      }
   }

   recordString += "\n";