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input_thread.h
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27 
28 // input_thread.h
29 //
30 
31 #pragma once
32 
33 #include "utils.h"
35 #include <nvbio/basic/console.h>
36 #include <nvbio/basic/timer.h>
37 #include <nvbio/basic/threads.h>
39 #include <stdio.h>
40 #include <stdlib.h>
41 
42 using namespace nvbio;
43 
46 
51 {
58  InputStageData(io::SequenceDataStream* file, const uint32 max_strings, const uint32 max_bps) :
59  m_file ( file ),
60  m_max_strings ( max_strings ),
61  m_max_bps ( max_bps ),
62  m_reads ( 0 ),
63  m_bps ( 0 ),
64  m_time ( 0.0f )
65  {}
66 
73  float m_time;
74 };
75 
79 struct InputStage
80 {
81  typedef void argument_type;
83 
90  InputStage() : m_data(NULL) {}
91 
98  InputStage(InputStageData* data) : m_data(data) {}
99 
102  bool process(PipelineContext& context)
103  {
104  m_data->m_mutex.lock();
105 
106  Timer timer;
107  timer.start();
108 
109  // fetch the output
110  io::SequenceDataHost* h_read_data = context.output<io::SequenceDataHost>();
111 
112  const int ret = io::next( DNA_N, h_read_data, m_data->m_file, m_data->m_max_strings, m_data->m_max_bps );
113 
114  timer.stop();
115  m_data->m_time += timer.seconds();
116  m_data->m_reads += h_read_data->size();
117  m_data->m_bps += h_read_data->bps();
118 
119  if (h_read_data->max_sequence_len() > MAX_READ_LENGTH)
120  {
121  log_error(stderr, " maximum read length exceeded: %u > %u\n", h_read_data->max_sequence_len(), MAX_READ_LENGTH);
122  return false;
123  }
124 
125  log_verbose(stderr, "\r loaded reads [%llu, %llu] (%.1fM / %.2fG bps, %.1fK reads/s, %.1fM bps/s) ",
126  m_data->m_reads,
127  m_data->m_reads + h_read_data->size(),
128  1.0e-6f * (h_read_data->bps()),
129  1.0e-9f * (m_data->m_bps + h_read_data->bps()),
130  m_data->m_time ? (1.0e-3f * (m_data->m_reads + h_read_data->size())) / m_data->m_time : 0.0f,
131  m_data->m_time ? (1.0e-6f * (m_data->m_bps + h_read_data->bps() )) / m_data->m_time : 0.0f );
132  log_debug_cont(stderr, "\n");
133 
134  m_data->m_mutex.unlock();
135 
136  return ret;
137  }
138 
140 };
141