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LibStatGen: BAM

4,054 bytes added, 14:51, 16 March 2010
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== 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.
This methods found in the SamRecord class for setting fields are:
{| class="wikitable" style="width:100%" border="1"
|+ style="font-size:150%"|'''SamFile Class Methods'''
! width=""|Method Name
! width=""|Description
|-
| bool setReadName(const char* readName)
| Sets QNAME to the passed in name.
Returns true if successfully set, false if not.
|-
| bool setFlag(int flag)
| Sets the bitwise FLAG to the passed in value.
Returns true if successfully set, false if not.
|-
| bool setReferenceID(int referenceID)
| 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.
Returns true if successfully set, false if not.
|-
| bool set1BasedPosition(int 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 set0BasedPosition(int 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 setMapQuality(int mapQuality)
| Sets the mapping quality.
Returns true if successfully set, false if not.
|-
| bool 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 setMateReferenceID(int mateReferenceID)
| 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.
Returns true if successfully set, false if not.
|-
| bool set1BasedMatePosition(int 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 set0BasedMatePosition(int 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 setInsertSize(int insertSize)
| Sets the inferred insert size.
Returns true if successfully set, false if not.
|-
| bool 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 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 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.
|}
 
 
== 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.

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