htslib 0.2.9 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c98f3937d65f091e9e834060f3a94578034d1bf55e7bc372e5ed388e618a6da4
-  data.tar.gz: 8e180044fef210935695bc60c0352b747b570b705f3ce9318b7538d19ddaf645
+  metadata.gz: ea68a4c331c9a404cfce2bf86fea386985e96ee3b76ae25e9d9b701593294880
+  data.tar.gz: d826e59f66e20bc40bc47c2033295abe2b3aceab8cb9d5af3d4d41309e448732
 SHA512:
-  metadata.gz: 5324913bdbe97580fee1e54b6268f22aed2a0b84d449c8a4f62529981c82a57d6ae5cea7cc77ff1be7332425eea259bfe5daa1107b6144e36ef40bb4997dd28f
-  data.tar.gz: 7b230700951223aeda09d64fac7cca44d734d54ec03a7836c5a0fb036e552854db80b9ecaf57aa478e317c684e4712f2f03244e02474fd2ea53a4b93346d1371
+  metadata.gz: 646dca4eb44c96a67020f57a090c26715b003521c9c6afffad1becf031576c334ea03c99b61f795a35932935535c53a1899a960ab986480cb3f5eef5b9913b96
+  data.tar.gz: e1cc5d9357932e04cebae1aaa5a8dc7024e0755584ea21999b18004dba76726c10b23276ee6d98fc1580ffb5aad45aeb12fd3e1bf94cfc45fdee70aefda87f91

data/README.md

@@ -6,6 +6,9 @@
 [![DOI](https://zenodo.org/badge/247078205.svg)](https://zenodo.org/badge/latestdoi/247078205)
 [![Docs Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/htslib)
 
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/kojix2/ruby-htslib)
+[![Lines of Code](https://img.shields.io/endpoint?url=https%3A%2F%2Ftokei.kojix2.net%2Fbadge%2Fgithub%2Fkojix2%2Fruby-htslib%2Flines)](https://tokei.kojix2.net/github/kojix2/ruby-htslib)
+
 Ruby-htslib is the [Ruby](https://www.ruby-lang.org) bindings to [HTSlib](https://github.com/samtools/htslib), a C library for high-throughput sequencing data formats. It allows you to read and write file formats commonly used in genomics, such as [SAM, BAM, VCF, and BCF](http://samtools.github.io/hts-specs/), in the Ruby language.
 
 :apple: Feel free to fork it!
@@ -162,6 +165,8 @@ Try Crystal. [HTS.cr](https://github.com/bio-cr/hts.cr) is implemented in Crysta
 
 ## Development
 
+![Diagram](diagram.svg)
+
 #### Compile from source code
 
 [GNU Autotools](https://en.wikipedia.org/wiki/GNU_Autotools) is required to compile htslib.

data/lib/hts/bam.rb

@@ -7,6 +7,8 @@ require_relative "bam/header"
 require_relative "bam/cigar"
 require_relative "bam/flag"
 require_relative "bam/record"
+# require_relative "bam/pileup"
+# require_relative "bam/pileup_entry"
 
 module HTS
   # A class for working with SAM, BAM, CRAM files.
@@ -30,7 +32,7 @@ module HTS
     def initialize(file_name, mode = "r", index: nil, fai: nil, threads: nil,
                    build_index: false)
       if block_given?
-        message = "HTS::Bam.new() dose not take block; Please use HTS::Bam.open() instead"
+        message = "HTS::Bam.new() does not take block; Please use HTS::Bam.open() instead"
         raise message
       end
 
@@ -44,6 +46,17 @@ module HTS
 
       raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null?
 
+      # Auto-detect and set reference for CRAM files
+      if fai.nil? && @file_name.end_with?(".cram")
+        # Try to find reference file in the same directory
+        base_name = File.basename(@file_name, ".cram")
+        dir_name = File.dirname(@file_name)
+        potential_ref = File.join(dir_name, "#{base_name}.fa")
+
+        # For remote URLs, assume reference exists; for local files, check existence
+        fai = potential_ref if @file_name.start_with?("http") || File.exist?(potential_ref)
+      end
+
       if fai
         r = LibHTS.hts_set_fai_filename(@hts_file, fai)
         raise "Failed to load fasta index: #{fai}" if r < 0
@@ -67,7 +80,7 @@ module HTS
       else
         warn "Create index for #{@file_name}"
       end
-      case LibHTS.sam_index_build3(@file_name, index_name, min_shift, (@nthreads || threads))
+      case LibHTS.sam_index_build3(@file_name, index_name, min_shift, @nthreads || threads)
       when 0 # successful
       when -1 then raise "indexing failed"
       when -2 then raise "opening #{@file_name} failed"
@@ -95,7 +108,7 @@ module HTS
     end
 
     def close
-      LibHTS.hts_idx_destroy(@idx) if @idx&.null?
+      LibHTS.hts_idx_destroy(@idx) if @idx && !@idx.null?
       @idx = nil
       super
     end
@@ -141,7 +154,7 @@ module HTS
     alias isize insert_size
     alias mpos mate_pos
 
-    # FXIME: experimental
+    # FIXME: experimental
     def aux(tag)
       check_closed
 
@@ -203,6 +216,10 @@ module HTS
       end
     end
 
+    # def pileup
+    #   Pileup.new(self)
+    # end
+
     private
 
     def queryi(tid, beg, end_, copy: false, &block)

data/lib/hts/bcf.rb

@@ -30,7 +30,7 @@ module HTS
     def initialize(file_name, mode = "r", index: nil, threads: nil,
                    build_index: false)
       if block_given?
-        message = "HTS::Bcf.new() dose not take block; Please use HTS::Bcf.open() instead"
+        message = "HTS::Bcf.new() does not take block; Please use HTS::Bcf.open() instead"
         raise message
       end
 
@@ -62,7 +62,7 @@ module HTS
       else
         warn "Create index for #{@file_name}"
       end
-      case LibHTS.bcf_index_build3(@file_name, index_name, min_shift, (@nthreads || threads))
+      case LibHTS.bcf_index_build3(@file_name, index_name, min_shift, @nthreads || threads)
       when 0 # successful
       when -1 then raise "indexing failed"
       when -2 then raise "opening #{@file_name} failed"
@@ -90,7 +90,7 @@ module HTS
     end
 
     def close
-      LibHTS.hts_idx_destroy(@idx) unless @idx&.null?
+      LibHTS.hts_idx_destroy(@idx) if @idx && !@idx.null?
       @idx = nil
       super
     end

data/lib/hts/faidx.rb

@@ -21,7 +21,7 @@ module HTS
 
     def initialize(file_name)
       if block_given?
-        message = "HTS::Faidx.new() dose not take block; Please use HTS::Faidx.open() instead"
+        message = "HTS::Faidx.new() does not take block; Please use HTS::Faidx.open() instead"
         raise message
       end
 

data/lib/hts/libhts/constants.rb

@@ -158,7 +158,7 @@ module HTS
         :specific,          :pointer
     end
 
-    class HtsIdx < FFI::Struct # FIXME: ManagedStruct
+    class HtsIdx < FFI::Struct
       layout \
         :fmt,            :int,
         :min_shift,      :int,
@@ -189,9 +189,9 @@ module HTS
           :n_unmapped,   :uint64
         )
 
-      def self.release(ptr)
-        LibHTS.hts_idx_destroy(ptr) unless ptr.null?
-      end
+      # def self.release(ptr)
+      #   LibHTS.hts_idx_destroy(ptr) unless ptr.null?
+      # end
     end
 
     class HtsReglist < FFI::Struct
@@ -379,6 +379,10 @@ module HTS
                  :is_refskip, 1,
                  :_reserved,  1,
                  :aux,        27
+
+      # def self.release(ptr)
+      #   LibHTS.bam_plp_destroy(ptr) unless ptr.null?
+      # end
     end
 
     class TbxConf < FFI::Struct

data/lib/hts/libhts/sam_funcs.rb

@@ -105,7 +105,7 @@ module HTS
 
       # Modifies a single base in the bam structure.
       def bam_set_seqi(s, i, b)
-        s[i >> 1] = (s[i >> 1] & (0xf0 >> ((~i & 1) << 2))) | ((b) << ((~i & 1) << 2))
+        s[i >> 1] = (s[i >> 1] & (0xf0 >> ((~i & 1) << 2))) | (b << ((~i & 1) << 2))
       end
 
       # Returns the SAM formatted text of the \@HD header line

data/lib/hts/libhts/vcf_funcs.rb

@@ -167,7 +167,7 @@ module HTS
 
       # Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based)
       def bcf_alleles2gt(a, b)
-        ((a) > (b) ? (a * (a + 1) / 2 + b) : (b * (b + 1) / 2 + a))
+        (a > b ? (a * (a + 1) / 2 + b) : (b * (b + 1) / 2 + a))
       end
 
       # Get INFO values

data/lib/hts/tabix.rb

@@ -24,7 +24,7 @@ module HTS
 
     def initialize(file_name, index: nil, threads: nil, build_index: false)
       if block_given?
-        message = "HTS::Tabix.new() dose not take block; Please use HTS::Tabix.open() instead"
+        message = "HTS::Tabix.new() does not take block; Please use HTS::Tabix.open() instead"
         raise message
       end
 

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.2.9"
+  VERSION = "0.3.0"
 end

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.2.9
+  version: 0.3.0
 platform: ruby
 authors:
 - kojix2
-autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-09-13 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -52,7 +51,6 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description:
 email:
 - 2xijok@gmail.com
 executables: []
@@ -104,7 +102,6 @@ licenses:
 - MIT
 metadata:
   msys2_mingw_dependencies: htslib
-post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -119,8 +116,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.11
-signing_key:
+rubygems_version: 3.7.1
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []