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fastq.cpp
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27 
28 #pragma once
29 
30 #include <nvbio/fastq/fastq.h>
31 #include <zlib/zlib.h>
32 
33 
34 namespace nvbio {
35 
37 {
38  Impl(const char* filename, const uint32 buffer_size)
39  {
40  m_file = gzopen( filename, "r" );
41 
42  if (m_file)
43  gzbuffer( m_file, buffer_size );
44  }
45 
47  {
48  if (m_file)
49  gzclose( m_file );
50  }
51 
53 };
54 
55 // constructor
56 //
57 FASTQ_gzfile::FASTQ_gzfile(const uint32 buffer_size) :
58  m_buffer( buffer_size ),
59  m_buffer_size( 0 ),
60  m_buffer_pos( 0 )
61 {
62  m_impl = NULL;
63 }
64 
65 // constructor
66 //
67 FASTQ_gzfile::FASTQ_gzfile(const char* filename, const uint32 buffer_size) :
68  m_buffer( buffer_size ),
69  m_buffer_size( 0 ),
70  m_buffer_pos( 0 )
71 {
72  m_impl = new Impl( filename, buffer_size );
73 }
74 
75 // destructor
76 //
77 FASTQ_gzfile::~FASTQ_gzfile() { delete m_impl; }
78 
79 // open a new file
80 //
81 void FASTQ_gzfile::open(const char* filename)
82 {
83  if (m_impl)
84  delete m_impl;
85 
86  m_impl = new Impl( filename, uint32( m_buffer.size() ) );
87 }
88 
89 // return whether the file is valid
90 //
91 bool FASTQ_gzfile::valid() const
92 {
93  return m_impl->m_file != NULL;
94 }
95 
96 // read a buffer
97 //
99 {
100  return gzread( m_impl->m_file, buffer, n );
101 }
102 
103 } // namespace nvbio