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output_bam.h
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27 
28 #pragma once
29 
30 #include <nvbio/io/output/output_types.h>
31 #include <nvbio/io/output/output_utils.h>
32 
33 #include <nvbio/io/output/output_file.h>
34 #include <nvbio/io/output/output_batch.h>
35 #include <nvbio/io/output/output_priv.h>
36 #include <nvbio/io/output/output_databuffer.h>
37 #include <nvbio/io/output/output_gzip.h>
38 #include <nvbio/io/sequence/sequence.h>
39 #include <nvbio/io/bam_format.h>
40 #include <nvbio/basic/threads.h>
41 #include <stdio.h>
42 
43 namespace nvbio {
44 namespace io {
45 
46 struct BamOutput : public OutputFile
47 {
48 private:
49  // BAM alignment flags
50  // these are meant to be bitwised OR'ed together
51  typedef enum {
52  BAM_FLAGS_PAIRED = 1 << 16,
53  BAM_FLAGS_PROPER_PAIR = 2 << 16,
54  BAM_FLAGS_UNMAPPED = 4 << 16,
55  BAM_FLAGS_MATE_UNMAPPED = 8 << 16,
56  BAM_FLAGS_REVERSE = 16 << 16,
57  BAM_FLAGS_MATE_REVERSE = 32 << 16,
58  BAM_FLAGS_READ_1 = 64 << 16,
59  BAM_FLAGS_READ_2 = 128 << 16,
60  BAM_FLAGS_SECONDARY = 256 << 16,
61  BAM_FLAGS_QC_FAILED = 512 << 16,
62  BAM_FLAGS_DUPLICATE = 1024 << 16
63  } BamAlignmentFlags;
64 
65 public:
66  BamOutput(const char *file_name, AlignmentType alignment_type, BNT bnt);
67  ~BamOutput();
68 
69  void header() { output_header(); }
70 
75  void process(struct HostOutputBatchSE& batch);
76 
81  void process(struct HostOutputBatchPE& batch);
82 
83  void close(void);
84 
85 private:
86  void output_header(void);
87  uint32 process_one_alignment(AlignmentData& alignment, AlignmentData& mate);
88 
89  void write_block();
90  void flush_blocks();
91 
92  uint32 generate_cigar(struct BAM_alignment& alnh,
93  struct BAM_alignment_data_block& alnd,
94  const AlignmentData& alignment);
95  uint32 generate_md_string(BAM_alignment& alnh, BAM_alignment_data_block& alnd,
96  const AlignmentData& alignment);
97 
98  void output_tag_uint32(DataBuffer& out, const char *tag, uint32 val);
99  void output_tag_uint8(DataBuffer& out, const char *tag, uint8 val);
100  void output_tag_string(DataBuffer& out, const char *tag, const char *val);
101 
102  void output_alignment(BAM_alignment& alnh, BAM_alignment_data_block& alnd);
103 
104  static uint8 encode_bp(uint8 bp);
105 
106  // our file pointer
107  FILE *fp;
108  // CPU copy of the current alignment batch
109  HostOutputBatchPE cpu_output;
110 
111  // text buffer that we're filling with data
112  static const uint32 BUFFERS = 64;
113  DataBuffer data_buffers[BUFFERS];
114  DataBuffer compressed_buffers[BUFFERS];
115  int32 buffer_id;
116 
117  // our BGZF compressors
118  BGZFCompressor bgzf[BUFFERS];
119 
120  Mutex mutex;
121 };
122 
123 } // namespace io
124 } // namespace nvbio
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