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bam.h
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27 
28 #pragma once
29 
30 #include <zlib/zlib.h>
31 
32 #include <nvbio/io/bam_format.h>
33 #include <nvbio/io/reads/reads.h>
35 #include <nvbio/basic/console.h>
36 
37 namespace nvbio {
38 namespace io {
39 
42 
45 
48 
52 {
55  ReadDataFile_BAM(const char *read_file_name,
56  const uint32 max_reads,
57  const uint32 max_read_len,
58  const ReadEncoding flags);
59 
62  virtual int nextChunk(ReadDataRAM *output, uint32 max_reads, uint32 max_bps);
63 
66  bool init(void);
67 
68 private:
71  bool readData(void *output, unsigned int len);
72 
73  // our file pointer
74  gzFile fp;
75 };
76 
80 
81 } // namespace io
82 } // namespace nvbio