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== Retrieving fields from a SAM/BAM Record ==
== 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.
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:
{| class="wikitable" style="width:100%" border="1"
|+ style="font-size:150%"|'''SamRecord Class Get Methods'''
! width=""|Method Name
! width=""|Description
|-
| int getBlockSize()
| Returns the BAM block size of the record.
|-
| int getReferenceID()
| Returns the reference sequence id (BAM format).
|-
| int get1BasedPosition()
| Returns the 1-based (SAM formatted) leftmost position.
|-
| int get0BasedPosition()
| Returns the 0-based (BAM formatted) leftmost position.
|-
| int getReadNameLength()
| Returns the length of the ReadName (QNAME).
|-
| int getMapQuality()
| Returns the map quality.
|-
| int getBin()
| Returns the BAM bin for the record.
|-
| int getCigarLength()
| Returns the length of the CIGAR in BAM format.
|-
| int getFlag()
| Returns the flag.
|-
| int getReadLength()
| Returns the length of the read.
|-
| int getMateReferenceID()
| Returns the mate reference sequence id (BAM format).
|-
| int get1BasedMatePosition()
| Returns the 1-based (SAM formatted) mate leftmost position.
|-
| int get0BasedMatePosition()
| Returns the 0-based (BAM formatted) mate leftmost position.
|-
| int getInsertSize()
| Returns the insert size.
|-
| const char* getReadName()
| Returns the SAM formatted Read Name (QNAME).
|-
| const char* getCigar()
| Returns the SAM formatted CIGAR string.
|-
| const char* getSequence()
| Returns the SAM formatted Sequence string.
|-
| const char* getQuality()
| Returns the SAM formatted Quality string.
|-
|}
