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input_thread.h
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27 
28 // input_thread.h
29 //
30 
31 #pragma once
32 
34 #include <nvbio/basic/console.h>
35 #include <nvbio/basic/timer.h>
36 #include <nvbio/basic/threads.h>
38 #include <stdio.h>
39 #include <stdlib.h>
40 
41 using namespace nvbio;
42 
46 struct InputStage
47 {
48  typedef void argument_type;
50 
57  InputStage(io::SequenceDataStream* file, const uint32 max_strings, const uint32 max_bps) :
58  m_file ( file ),
59  m_max_strings ( max_strings ),
60  m_max_bps ( max_bps )
61  {}
62 
65  bool process(PipelineContext& context)
66  {
67  Timer timer;
68  timer.start();
69 
70  // fetch the output
72 
73  log_debug(stderr, " loading.. started (%u, %u)\n", m_max_strings, m_max_bps);
74  const int ret = io::next( DNA, output, m_file, m_max_strings, m_max_bps );
75  log_debug(stderr, " loading.. done\n");
76 
77  timer.stop();
78  m_time += timer.seconds();
79  return ret;
80  }
81 
85  float m_time;
86 };