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, 15:53, 16 March 2010
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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. |
| + | |- |
| + | |} |