Class: HTS::Bam

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/hts/bam.rb,
lib/hts/bam/flag.rb,
lib/hts/bam/cigar.rb,
lib/hts/bam/header.rb,
lib/hts/bam/record.rb

Defined Under Namespace

Classes: Cigar, Flag, Header, Record

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filename, mode = "r", fai: nil, threads: nil, index: nil) ⇒ Bam

Returns a new instance of Bam.



29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
 
# File 'lib/hts/bam.rb', line 29

def initialize(filename, mode = "r", fai: nil, threads: nil, index: nil)
  raise "HTS::Bam.new() dose not take block; Please use HTS::Bam.open() instead" if block_given?

  @file_path = filename == "-" ? "-" : File.expand_path(filename)

  if mode[0] == "r" && !File.exist?(file_path)
    message = "No such SAM/BAM file - #{file_path}"
    raise message
  end

  @mode      = mode
  @hts_file  = LibHTS.hts_open(file_path, mode)

  if fai
    fai_path = File.expand_path(fai)
    r = LibHTS.hts_set_fai_filename(@hts_file, fai_path)
    raise "Failed to load fasta index: #{fai}" if r < 0
  end

  if threads&.> 0
    r = LibHTS.hts_set_threads(@hts_file, threads)
    raise "Failed to set number of threads: #{threads}" if r < 0
  end

  return if mode[0] == "w"

  @header = Bam::Header.new(@hts_file)

  create_index if index

  # load index
  @idx = LibHTS.sam_index_load(@hts_file, file_path)
end

Instance Attribute Details

#file_path ⇒ Object (readonly)

Returns the value of attribute file_path.



15
16
17
 
# File 'lib/hts/bam.rb', line 15

def file_path
  @file_path
end

#header ⇒ Object (readonly)

Returns the value of attribute header.



15
16
17
 
# File 'lib/hts/bam.rb', line 15

def header
  @header
end

#mode ⇒ Object (readonly)

Returns the value of attribute mode.



15
16
17
 
# File 'lib/hts/bam.rb', line 15

def mode
  @mode
end

Class Method Details

.open ⇒ Object 



17
18
19
20
21
22
23
24
25
26
27
 
# File 'lib/hts/bam.rb', line 17

def self.open(...)
  file = new(...)
  return file unless block_given?

  begin
    yield file
  ensure
    file.close
  end
  file
end

Instance Method Details

#close ⇒ Object

Close the current file.



79
80
81
82
83
84
 
# File 'lib/hts/bam.rb', line 79

def close
  LibHTS.hts_idx_destroy(@idx) if @idx
  @idx = nil
  LibHTS.hts_close(@hts_file)
  @hts_file = nil
end

#closed? ⇒ Boolean

Returns:

  • (Boolean) 


86
87
88
 
# File 'lib/hts/bam.rb', line 86

def closed?
  @hts_file.nil?
end

#create_index ⇒ Object 



63
64
65
66
67
68
 
# File 'lib/hts/bam.rb', line 63

def create_index
  warn "Create index for #{file_path}"
  LibHTS.sam_index_build(file_path, -1)
  idx = LibHTS.sam_index_load(@hts_file, file_path)
  raise "Failed to load index: #{file_path}" if idx.null?
end

#each ⇒ Object

Iterate over each record. Record object is reused. Faster than each_copy.



109
110
111
112
113
114
115
116
117
118
 
# File 'lib/hts/bam.rb', line 109

def each
  # Each does not always start at the beginning of the file.
  # This is the common behavior of IO objects in Ruby.
  # This may change in the future.
  return to_enum(__method__) unless block_given?

  bam1 = LibHTS.bam_init1
  record = Record.new(bam1, header)
  yield record while LibHTS.sam_read1(@hts_file, header, bam1) > 0
end

#each_copy ⇒ Object

Iterate over each record. Generate a new Record object each time. Slower than each.



123
124
125
126
127
128
129
130
 
# File 'lib/hts/bam.rb', line 123

def each_copy
  return to_enum(__method__) unless block_given?

  while LibHTS.sam_read1(@hts_file, header, bam1 = LibHTS.bam_init1) > 0
    record = Record.new(bam1, header)
    yield record
  end
end

#flush ⇒ Object

Flush the current file.



102
103
104
 
# File 'lib/hts/bam.rb', line 102

def flush
  # LibHTS.bgzf_flush(@@hts_file.fp.bgzf)
end

#query(region) ⇒ Object

query [WIP]



133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
 
# File 'lib/hts/bam.rb', line 133

def query(region)
  # FIXME: when @idx is nil
  qiter = LibHTS.sam_itr_querys(@idx, header, region)
  begin
    bam1 = LibHTS.bam_init1
    slen = LibHTS.sam_itr_next(@hts_file, qiter, bam1)
    while slen > 0
      yield Record.new(bam1, header)
      bam1 = LibHTS.bam_init1
      slen = LibHTS.sam_itr_next(@hts_file, qiter, bam1)
    end
  ensure
    LibHTS.hts_itr_destroy(qiter)
  end
end

#struct ⇒ Object 



70
71
72
 
# File 'lib/hts/bam.rb', line 70

def struct
  @hts_file
end

#to_ptr ⇒ Object 



74
75
76
 
# File 'lib/hts/bam.rb', line 74

def to_ptr
  @hts_file.to_ptr
end

#write(aln) ⇒ Object 



96
97
98
99
 
# File 'lib/hts/bam.rb', line 96

def write(aln)
  aln_dup = aln.dup
  LibHTS.sam_write1(@hts_file, header, aln_dup) > 0 || raise
end

#write_header(header) ⇒ Object 



90
91
92
93
94
 
# File 'lib/hts/bam.rb', line 90

def write_header(header)
  @header = header.dup
  LibHTS.hts_set_fai_filename(@hts_file, @file_path)
  LibHTS.sam_hdr_write(@hts_file, header)
end