htslib 0.2.5 → 0.2.6

data/lib/hts/tbx.rb

@@ -59,6 +59,10 @@ module HTS
       end
     end
 
+    def index_loaded?
+      !@idx.null?
+    end
+
     def tid(name)
       LibHTS.tbx_name2id(@idx, name)
     end
@@ -69,5 +73,50 @@ module HTS
         pts.read_array_of_pointer(nseq.read_int).map(&:read_string)
       end
     end
+
+    def query(region, start = nil, end_ = nil, &block)
+      check_closed
+      raise "Index file is required to call the query method." unless index_loaded?
+
+      if start && end_
+        queryi(tid(region), start, end_, &block)
+      else
+        querys(region, &block)
+      end
+    end
+
+    private
+
+    def queryi(id, start, end_)
+      return to_enum(__method__, id, start, end_) unless block_given?
+
+      qiter = LibHTS.tbx_itr_queryi(@idx, id, start, end_)
+
+      raise "Failed to query region: #{id}:#{start}-#{end_}" if qiter.null?
+
+      r = LibHTS::KString.new
+      begin
+        yield r[:s] while LibHTS.tbx_itr_next(@hts_file, @idx, qiter, r) > 0
+      ensure
+        LibHTS.hts_itr_destroy(qiter)
+      end
+      self
+    end
+
+    def querys(region)
+      return to_enum(__method__, region) unless block_given?
+
+      qiter = LibHTS.tbx_itr_querys(@idx, region)
+
+      raise "Failed to query region: #{region}" if qiter.null?
+
+      r = LibHTS::KString.new
+      begin
+        yield r[:s].split("\t") while LibHTS.tbx_itr_next(@hts_file, @idx, qiter, r) > 0
+      ensure
+        LibHTS.hts_itr_destroy(qiter)
+      end
+      self
+    end
   end
 end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.2.5"
+  VERSION = "0.2.6"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.2.5
+  version: 0.2.6
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-10-27 00:00:00.000000000 Z
+date: 2023-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -131,6 +131,7 @@ extra_rdoc_files: []
 files:
 - LICENSE.txt
 - README.md
+- TUTORIAL.md
 - lib/hts/bam.rb
 - lib/hts/bam/auxi.rb
 - lib/hts/bam/cigar.rb
@@ -145,6 +146,7 @@ files:
 - lib/hts/bcf/info.rb
 - lib/hts/bcf/record.rb
 - lib/hts/faidx.rb
+- lib/hts/faidx/sequence.rb
 - lib/hts/ffi_ext/README.md
 - lib/hts/ffi_ext/pointer.rb
 - lib/hts/ffi_ext/struct.rb
@@ -187,7 +189,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.7
+rubygems_version: 3.4.1
 signing_key: 
 specification_version: 4
 summary: HTSlib bindings for Ruby