Class: HTS::Bam
- Includes:
- Enumerable
- Defined in:
- lib/hts/bam.rb,
lib/hts/bam/aux.rb,
lib/hts/bam/flag.rb,
lib/hts/bam/cigar.rb,
lib/hts/bam/header.rb,
lib/hts/bam/record.rb
Overview
A class for working with SAM, BAM, CRAM files.
Defined Under Namespace
Classes: Aux, Cigar, Flag, Header, Record
Instance Attribute Summary collapse
-
#file_name ⇒ Object
readonly
Returns the value of attribute file_name.
-
#header ⇒ Object
readonly
Returns the value of attribute header.
-
#index_name ⇒ Object
readonly
Returns the value of attribute index_name.
-
#mode ⇒ Object
readonly
Returns the value of attribute mode.
-
#nthreads ⇒ Object
readonly
Returns the value of attribute nthreads.
Class Method Summary collapse
Instance Method Summary collapse
- #aux(tag) ⇒ Object
- #build_index(index_name = nil, min_shift: 0) ⇒ Object
-
#chrom ⇒ Array
Get chrom array.
-
#cigar ⇒ Array
Get cigar array.
-
#close ⇒ Object
Close the current file.
- #each(copy: false, &block) ⇒ Object
- #each_aux(tag) ⇒ Object
-
#each_chrom ⇒ Object
Get chrom iterator.
-
#each_cigar ⇒ Object
Get cigar iterator.
-
#each_flag ⇒ Object
Get flag iterator.
-
#each_insert_size ⇒ Object
(also: #each_isize)
Get insert_size iterator.
-
#each_mapq ⇒ Object
Get mapq iterator.
-
#each_mate_chrom ⇒ Object
Get mate_chrom iterator.
-
#each_mate_pos ⇒ Object
(also: #each_mpos)
Get mate_pos iterator.
-
#each_pos ⇒ Object
Get pos iterator.
-
#each_qname ⇒ Object
Get qname iterator.
-
#each_qual ⇒ Object
Get qual iterator.
-
#each_seq ⇒ Object
Get seq iterator.
-
#flag ⇒ Array
Get flag array.
- #index_loaded? ⇒ Boolean
-
#initialize(file_name, mode = "r", index: nil, fai: nil, threads: nil, build_index: false) ⇒ Bam
constructor
A new instance of Bam.
-
#insert_size ⇒ Array
(also: #isize)
Get insert_size array.
- #load_index(index_name = nil) ⇒ Object
-
#mapq ⇒ Array
Get mapq array.
-
#mate_chrom ⇒ Array
Get mate_chrom array.
-
#mate_pos ⇒ Array
(also: #mpos)
Get mate_pos array.
-
#pos ⇒ Array
Get pos array.
-
#qname ⇒ Array
Get qname array.
-
#qual ⇒ Array
Get qual array.
- #query(region, copy: false, &block) ⇒ Object
-
#seq ⇒ Array
Get seq array.
- #write(aln) ⇒ Object
- #write_header(header) ⇒ Object
Methods inherited from Hts
#closed?, #file_format, #file_format_version, #rewind, #seek, #set_threads, #struct, #tell, #to_ptr
Constructor Details
#initialize(file_name, mode = "r", index: nil, fai: nil, threads: nil, build_index: false) ⇒ Bam
Returns a new instance of Bam.
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 30 def initialize(file_name, mode = "r", index: nil, fai: nil, threads: nil, build_index: false) if block_given? = "HTS::Bam.new() dose not take block; Please use HTS::Bam.open() instead" raise end # NOTE: Do not check for the existence of local files, since file_names may be remote URIs. @file_name = file_name @index_name = index @mode = mode @nthreads = threads @hts_file = LibHTS.hts_open(@file_name, mode) raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null? if fai r = LibHTS.hts_set_fai_filename(@hts_file, fai) raise "Failed to load fasta index: #{fai}" if r < 0 end set_threads(threads) if threads return if @mode[0] == "w" @header = Bam::Header.new(@hts_file) build_index(index) if build_index @idx = load_index(index) @start_position = tell super # do nothing end |
Instance Attribute Details
#file_name ⇒ Object (readonly)
Returns the value of attribute file_name.
16 17 18 |
# File 'lib/hts/bam.rb', line 16 def file_name @file_name end |
#header ⇒ Object (readonly)
Returns the value of attribute header.
16 17 18 |
# File 'lib/hts/bam.rb', line 16 def header @header end |
#index_name ⇒ Object (readonly)
Returns the value of attribute index_name.
16 17 18 |
# File 'lib/hts/bam.rb', line 16 def index_name @index_name end |
#mode ⇒ Object (readonly)
Returns the value of attribute mode.
16 17 18 |
# File 'lib/hts/bam.rb', line 16 def mode @mode end |
#nthreads ⇒ Object (readonly)
Returns the value of attribute nthreads.
16 17 18 |
# File 'lib/hts/bam.rb', line 16 def nthreads @nthreads end |
Class Method Details
.open(*args, **kw) ⇒ Object
18 19 20 21 22 23 24 25 26 27 28 |
# File 'lib/hts/bam.rb', line 18 def self.open(*args, **kw) file = new(*args, **kw) # do not yield return file unless block_given? begin yield file ensure file.close end file end |
Instance Method Details
#aux(tag) ⇒ Object
212 213 214 215 216 217 218 219 |
# File 'lib/hts/bam.rb', line 212 def aux(tag) warn "experimental" check_closed position = tell ary = map { |r| r.aux(tag) } seek(position) ary end |
#build_index(index_name = nil, min_shift: 0) ⇒ Object
63 64 65 66 67 68 69 70 71 72 73 74 75 |
# File 'lib/hts/bam.rb', line 63 def build_index(index_name = nil, min_shift: 0) check_closed if index_name warn "Create index for #{@file_name} to #{index_name}" else warn "Create index for #{@file_name}" end r = LibHTS.sam_index_build3(@file_name, index_name, min_shift, @nthreads) raise "Failed to build index for #{@file_name}" if r < 0 self end |
#chrom ⇒ Array
Get chrom array
199 |
# File 'lib/hts/bam.rb', line 199 define_getter :chrom |
#cigar ⇒ Array
Get cigar array
202 |
# File 'lib/hts/bam.rb', line 202 define_getter :cigar |
#close ⇒ Object
Close the current file.
94 95 96 97 98 |
# File 'lib/hts/bam.rb', line 94 def close LibHTS.hts_idx_destroy(@idx) if @idx&.null? @idx = nil super end |
#each(copy: false, &block) ⇒ Object
115 116 117 118 119 120 121 |
# File 'lib/hts/bam.rb', line 115 def each(copy: false, &block) if copy each_record_copy(&block) else each_record_reuse(&block) end end |
#each_aux(tag) ⇒ Object
239 240 241 242 243 244 245 246 247 248 249 |
# File 'lib/hts/bam.rb', line 239 def each_aux(tag) warn "experimental" check_closed return to_enum(__method__, tag) unless block_given? each do |record| yield record.aux(tag) end self end |
#each_chrom ⇒ Object
Get chrom iterator
226 |
# File 'lib/hts/bam.rb', line 226 define_iterator :chrom |
#each_cigar ⇒ Object
Get cigar iterator
229 |
# File 'lib/hts/bam.rb', line 229 define_iterator :cigar |
#each_flag ⇒ Object
Get flag iterator
225 |
# File 'lib/hts/bam.rb', line 225 define_iterator :flag |
#each_insert_size ⇒ Object Also known as: each_isize
Get insert_size iterator
232 |
# File 'lib/hts/bam.rb', line 232 define_iterator :insert_size |
#each_mapq ⇒ Object
Get mapq iterator
228 |
# File 'lib/hts/bam.rb', line 228 define_iterator :mapq |
#each_mate_chrom ⇒ Object
Get mate_chrom iterator
230 |
# File 'lib/hts/bam.rb', line 230 define_iterator :mate_chrom |
#each_mate_pos ⇒ Object Also known as: each_mpos
Get mate_pos iterator
231 |
# File 'lib/hts/bam.rb', line 231 define_iterator :mate_pos |
#each_pos ⇒ Object
Get pos iterator
227 |
# File 'lib/hts/bam.rb', line 227 define_iterator :pos |
#each_qname ⇒ Object
Get qname iterator
224 |
# File 'lib/hts/bam.rb', line 224 define_iterator :qname |
#each_qual ⇒ Object
Get qual iterator
234 |
# File 'lib/hts/bam.rb', line 234 define_iterator :qual |
#each_seq ⇒ Object
Get seq iterator
233 |
# File 'lib/hts/bam.rb', line 233 define_iterator :seq |
#flag ⇒ Array
Get flag array
198 |
# File 'lib/hts/bam.rb', line 198 define_getter :flag |
#index_loaded? ⇒ Boolean
87 88 89 90 91 |
# File 'lib/hts/bam.rb', line 87 def index_loaded? check_closed !@idx.null? end |
#insert_size ⇒ Array Also known as: isize
Get insert_size array
205 |
# File 'lib/hts/bam.rb', line 205 define_getter :insert_size |
#load_index(index_name = nil) ⇒ Object
77 78 79 80 81 82 83 84 85 |
# File 'lib/hts/bam.rb', line 77 def load_index(index_name = nil) check_closed if index_name LibHTS.sam_index_load2(@hts_file, @file_name, index_name) else LibHTS.sam_index_load3(@hts_file, @file_name, nil, 2) # should be 3 ? (copy remote file to local?) end end |
#mapq ⇒ Array
Get mapq array
201 |
# File 'lib/hts/bam.rb', line 201 define_getter :mapq |
#mate_chrom ⇒ Array
Get mate_chrom array
203 |
# File 'lib/hts/bam.rb', line 203 define_getter :mate_chrom |
#mate_pos ⇒ Array Also known as: mpos
Get mate_pos array
204 |
# File 'lib/hts/bam.rb', line 204 define_getter :mate_pos |
#pos ⇒ Array
Get pos array
200 |
# File 'lib/hts/bam.rb', line 200 define_getter :pos |
#qname ⇒ Array
Get qname array
197 |
# File 'lib/hts/bam.rb', line 197 define_getter :qname |
#qual ⇒ Array
Get qual array
207 |
# File 'lib/hts/bam.rb', line 207 define_getter :qual |
#query(region, copy: false, &block) ⇒ Object
146 147 148 149 150 151 152 |
# File 'lib/hts/bam.rb', line 146 def query(region, copy: false, &block) if copy query_copy(region, &block) else query_reuse(region, &block) end end |
#seq ⇒ Array
Get seq array
206 |
# File 'lib/hts/bam.rb', line 206 define_getter :seq |
#write(aln) ⇒ Object
108 109 110 111 112 113 |
# File 'lib/hts/bam.rb', line 108 def write(aln) check_closed aln_dup = aln.dup LibHTS.sam_write1(@hts_file, header, aln_dup) > 0 || raise end |
#write_header(header) ⇒ Object
100 101 102 103 104 105 106 |
# File 'lib/hts/bam.rb', line 100 def write_header(header) check_closed @header = header.dup LibHTS.hts_set_fai_filename(@hts_file, @file_name) LibHTS.sam_hdr_write(@hts_file, header) end |