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= SAM/BAM File=
== Reading/Writing SAM/BAM Files ==
The SamFile class allows a user to easily read/write a SAM/BAM file.
This methods found in this class are:
{| class="wikitable" style="width:100%" border="1"
|+ style="font-size:150%"|'''SamFile Class Methods'''
! width=""|Method Name
! width=""|Description
|-
| bool OpenForRead(const char* filename)
| Opens the specified file for reading.
Determines if it is a BAM/SAM file by reading the beginning of the file.
Returns true if successfully opened reading, false if not.
|-
| bool OpenForWrite(const char * filename)
| bool: true if successfully opened, false if not.
Opens as BAM file if the specified filename ends in .bam. Otherwise it is opened as a SAM file.
Returns true if successfully opened for writing, false if not.
|-
| bool ReadHeader(SamFileHeader& header)
| Reads the header section from the file and stores it in the passed in header.
Returns true if successfully read, false if not.
|-
| bool WriteHeader(const SamFileHeader& header)
| Writes the specified header into the file.
Returns true if successfully written, false if not.
|-
| bool ReadRecord(SamFileHeader& header, SamRecord& record)
| Reads the next record from the file and stores it in the passed in record.
Returns true if successfully read, false if not.
|-
| bool WriteRecord(SamFileHeader& header, SamRecord& record)
| Writes the specified record into the file.
Returns true if successfully written, false if not.
|}
== Reading/Writing SAM/BAM Files ==
The SamFile class allows a user to easily read/write a SAM/BAM file.
This methods found in this class are:
{| class="wikitable" style="width:100%" border="1"
|+ style="font-size:150%"|'''SamFile Class Methods'''
! width=""|Method Name
! width=""|Description
|-
| bool OpenForRead(const char* filename)
| Opens the specified file for reading.
Determines if it is a BAM/SAM file by reading the beginning of the file.
Returns true if successfully opened reading, false if not.
|-
| bool OpenForWrite(const char * filename)
| bool: true if successfully opened, false if not.
Opens as BAM file if the specified filename ends in .bam. Otherwise it is opened as a SAM file.
Returns true if successfully opened for writing, false if not.
|-
| bool ReadHeader(SamFileHeader& header)
| Reads the header section from the file and stores it in the passed in header.
Returns true if successfully read, false if not.
|-
| bool WriteHeader(const SamFileHeader& header)
| Writes the specified header into the file.
Returns true if successfully written, false if not.
|-
| bool ReadRecord(SamFileHeader& header, SamRecord& record)
| Reads the next record from the file and stores it in the passed in record.
Returns true if successfully read, false if not.
|-
| bool WriteRecord(SamFileHeader& header, SamRecord& record)
| Writes the specified record into the file.
Returns true if successfully written, false if not.
|}
