Changes

| Reads the next record from the file and stores it in the passed in record.   

| Reads the next record from the file and stores it in the passed in record.   

If it is an indexed BAM file and SetReadSection was called, only alignments in the section specified by SetReadSection are read.  If they all have already been read, this method returns false.

If it is an indexed BAM file and SetReadSection was called, only alignments in the section specified by <code>SetReadSection</code> are read.  If they all have already been read, this method returns false.

Validates that the record is sorted according to the value set by <code>setSortedValidation</code>.  No sorting validation is done if specified to be unsorted, or <code>setSortedValidation</code> was never called.

Validates that the record is sorted according to the value set by <code>setSortedValidation</code>.  No sorting validation is done if specified to be unsorted, or <code>setSortedValidation</code> was never called.

|-

|-

| <code>bool SamFile::SetReadSection(int32_t refID)</code>

| <code>bool SamFile::SetReadSection(int32_t refID)</code>

| Tell the class which reference ID should be read from the BAM file.  This is the index into the BAM Index list of reference information: 0 - #references.  The records for that reference id will be retrieved on each ReadRecord call.  When all records have been retrieved for the specified reference id, ReadRecord will return false until a new read section is set.

| Tell the class which reference ID should be read from the BAM file.  This is the index into the BAM Index list of reference information: 0 - #references.  The records for that reference id will be retrieved on each <code>ReadRecord</code> call.  When all records have been retrieved for the specified reference id, <code>ReadRecord</code> will return false until a new read section is set.

Pass in -1 in order to read the section of the bam file not associated with any reference ID.

Pass in -1 in order to read the section of the bam file not associated with any reference ID.

Returns true if the read section was successfully set, false if not.  False is returned if the BAM Index File has not yet been read or if a BAM file is not open for reading.

Returns true if the read section was successfully set, false if not.  False is returned if the BAM Index File has not yet been read or if a BAM file is not open for reading.

                   const char* indexFilename)

                   const char* indexFilename)

{

{

   IndexedBamReader samIn;

   SamFile samIn;

        

        

   samIn.OpenForRead(inputFilename, indexFilename);

   samIn.OpenForRead(inputFilename);

  samIn.ReadBamIndex(indexFilename);

   SamFile samOut;

   SamFile samOut;