Changes

==== Usage Example ====

==== Usage Example ====

This example reads in the inputFilename bam file and writes it back out section by section to the specified outputFilename, starting with section -1.  It also prints a count of the number of records in each section.

This example reads in the inputFilename bam file and writes it back out section by section to the specified outputFilename, starting with section -1.  It also prints a count of the number of records in each section.

<pre>

<source lang="cpp">

int ReadIndexedBam(const char* inputFilename,

int ReadIndexedBam(const char* inputFilename,

                   const char* outputFilename,

                   const char* outputFilename,

   return(0);

   return(0);

}

}

</pre>

</source>

Example of using getNextSamTag:

Example of using getNextSamTag:

<pre>

<source lang="cpp">

   // record is a previously setup SamRecord.

   // record is a previously setup SamRecord.

   String recordString = "";

   String recordString = "";

   recordString += "\n";

   recordString += "\n";

</pre>

</source>

== Suggested Improvements/Features ==

== Suggested Improvements/Features ==

* Add optional user flag for checking if a file is sorted when it is read.  It would report an error if it is unsorted.

* Add optional user flag for checking if a file is sorted when it is read.  It would report an error if it is unsorted.