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=== Reading/Writing Standard SAM/BAM Files ===

=== Reading/Writing Standard SAM/BAM Files ===

The SamFile class allows a user to easily read/write a SAM/BAM file.

The '''SamFile''' class allows a user to easily read/write a SAM/BAM file.

The methods found in this class are:

The methods found in this class are:

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==== Usage Example ====

==== Usage Example ====

The following example reads in a sam/bam file and writes it out as a sam/bam file.  The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file.  The file format of the output sam/bam file is determined by the SamFile class based on the extension of the output file.  A ".bam" extension indicates a BAM file.  All other extensions indicate SAM files.

The following example reads in a sam/bam file and writes it out as a sam/bam file.  The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file.  The file format of the output sam/bam file is determined by the '''SamFile''' class based on the extension of the output file.  A ".bam" extension indicates a BAM file.  All other extensions indicate SAM files.

<pre>

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int main(int argc, char ** argv)

int main(int argc, char ** argv)

=== Reading Indexed (and Sorted) BAM Files ===

=== Reading Indexed (and Sorted) BAM Files ===

The IndexedBamReader class allows a user to easily read BAM files that are sorted and indexed.

The '''IndexedBamReader''' class allows a user to easily read BAM files that are sorted and indexed.

This class allows a user to read only alignments for specific reference sequence.  This saves the time of having to read the entire file.

This class allows a user to read only alignments for specific reference sequence.  This saves the time of having to read the entire file.

It takes advantage of the seeking capability of BGZF files, using the BAM Index file to determine where in the BAM file to seek to.

It takes advantage of the seeking capability of BGZF files, using the BAM Index file to determine where in the BAM file to seek to.

== Setting fields in a SAM/BAM Header ==

== Setting fields in a SAM/BAM Header ==

The SamRecord class contains accessors to set the header lines of a SAM/BAM header.  By using these set methods to setup the header, they can be pulled back out using the get accessors or the header can be later written to a SAM/BAM file.   

The '''SamRecord''' class contains accessors to set the header lines of a SAM/BAM header.  By using these set methods to setup the header, they can be pulled back out using the get accessors or the header can be later written to a SAM/BAM file.   

The methods found in the SamFileHeader class for setting fields are:

The methods found in the '''SamFileHeader''' class for setting fields are:

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|+ style="font-size:150%"|'''SamFileHeader Class Methods'''

|+ style="font-size:150%"|'''SamFileHeader Class Methods'''

== Setting fields in a SAM/BAM Record ==

== 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.   

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.   

The methods found in the SamRecord class for setting fields are:

The methods found in the '''SamRecord''' class for setting fields are:

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|+ style="font-size:150%"|'''SamRecord Class Methods'''

|+ style="font-size:150%"|'''SamRecord Class Methods'''

== 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.  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 '''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:

The methods found in the SamRecord class for setting fields are: