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// Successfully read a record from the file, so check to see
// Successfully read a record from the file, so check to see
// if it is valid.
// if it is valid.
if(samRecord.isValid())
if(samRecord.isValid(samHeader))
{
{
// It is valid, so write it.
// It is valid, so write it.
// Successfully read a record from the file, so check to see
// Successfully read a record from the file, so check to see
// if it is valid.
// if it is valid.
if(samRecord.isValid())
if(samRecord.isValid(samHeader))
{
{
// It is valid, so write it.
// It is valid, so write it.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
|-
|-
| bool setReferenceID(int referenceID)
| bool setReferenceName(SamFileHeader& header, const char* referenceName)
| 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.
| Sets the reference sequence name. The reference id is calculated using the header.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
|-
|-
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
|-
|-
| bool setMateReferenceID(int mateReferenceID)
| bool setMateReferenceName(SamFileHeader& header, const char* referenceName)
| 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.
| Sets the mate reference sequence name. The mate reference id is calculated using the header.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
|-
|-
! width=""|Description
! width=""|Description
|-
|-
| bool isValid()
| bool 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.
| 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.
|-
|-
| int getBlockSize()
| int getBlockSize()
| Returns the BAM block size of the record.
| Returns the BAM block size of the record.
|-
| const char* getReferenceName()
| Returns the reference sequence name (SAM format).
|-
|-
| int getReferenceID()
| int getReferenceID()
| Returns the reference sequence id (BAM format).
| Returns the reference sequence ID (BAM format).
|-
|-
| int get1BasedPosition()
| int get1BasedPosition()
| int getReadLength()
| int getReadLength()
| Returns the length of the read.
| Returns the length of the read.
|-
| const char* getMateReferenceName()
| 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* getMateReferenceNameOrEqual()
| 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..
|-
|-
| int getMateReferenceID()
| int getMateReferenceID()
