indexed_sam_reader.h File Reference

#include "indexed_sam_iterator.h"
#include "../exceptions.h"
#include "../utils/hts_memory.h"
#include "htslib/sam.h"
#include <string>
#include <iostream>
#include <fstream>
#include <memory>
#include <vector>

Go to the source code of this file.

Classes
class	gamgee::IndexedSamReader< ITERATOR >
	Utility class to read a BAM/CRAM file with an appropriate Sam iterator from an indexed file in a for-each loop. Intervals are passed in using a vector of string coordinates compatible with Samtools. When iteration begins, the iterations (re-)starts at the beginning of the first interval. More...

Namespaces
	gamgee

Typedefs
using	gamgee::IndexedSingleSamReader = IndexedSamReader< IndexedSamIterator >