htslib 0.4.2 → 0.5.0

data/lib/hts/libhts/sam_funcs.rb

@@ -1,155 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    # constants
-    BAM_CMATCH     = 0
-    BAM_CINS       = 1
-    BAM_CDEL       = 2
-    BAM_CREF_SKIP  = 3
-    BAM_CSOFT_CLIP = 4
-    BAM_CHARD_CLIP = 5
-    BAM_CPAD       = 6
-    BAM_CEQUAL     = 7
-    BAM_CDIFF      = 8
-    BAM_CBACK      = 9
-
-    BAM_CIGAR_STR = "MIDNSHP=XB"
-    BAM_CIGAR_SHIFT = 4
-    BAM_CIGAR_MASK  = 0xf
-    BAM_CIGAR_TYPE  = 0x3C1A7
-
-    # macros
-    class << self
-      def bam_cigar_op(c)
-        c & BAM_CIGAR_MASK
-      end
-
-      def bam_cigar_oplen(c)
-        c >> BAM_CIGAR_SHIFT
-      end
-
-      def bam_cigar_opchr(c)
-        "#{BAM_CIGAR_STR}??????"[bam_cigar_op(c)]
-      end
-
-      def bam_cigar_gen(l, o)
-        (l << BAM_CIGAR_SHIFT) | o
-      end
-
-      def bam_cigar_type(o)
-        (BAM_CIGAR_TYPE >> (o << 1)) & 3
-      end
-    end
-
-    BAM_FPAIRED        =    1
-    BAM_FPROPER_PAIR   =    2
-    BAM_FUNMAP         =    4
-    BAM_FMUNMAP        =    8
-    BAM_FREVERSE       =   16
-    BAM_FMREVERSE      =   32
-    BAM_FREAD1         =   64
-    BAM_FREAD2         =  128
-    BAM_FSECONDARY     =  256
-    BAM_FQCFAIL        =  512
-    BAM_FDUP           = 1024
-    BAM_FSUPPLEMENTARY = 2048
-
-    # macros
-    # function-like macros
-    class << self
-      # Get whether the query is on the reverse strand
-      def bam_is_rev(b)
-        b[:core][:flag] & BAM_FREVERSE != 0
-      end
-
-      # Get whether the query's mate is on the reverse strand
-      def bam_is_mrev(b)
-        b[:core][:flag] & BAM_FMREVERSE != 0
-      end
-
-      # Get the name of the query
-      def bam_get_qname(b)
-        b[:data]
-      end
-
-      # Get the CIGAR array
-      def bam_get_cigar(b)
-        b[:data] + b[:core][:l_qname]
-      end
-
-      # Get query sequence
-      def bam_get_seq(b)
-        b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname]
-      end
-
-      # Get query quality
-      def bam_get_qual(b)
-        b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname] + ((b[:core][:l_qseq] + 1) >> 1)
-      end
-
-      # Get auxiliary data
-      def bam_get_aux(b)
-        b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname] + ((b[:core][:l_qseq] + 1) >> 1) + b[:core][:l_qseq]
-      end
-
-      # Get length of auxiliary data
-      def bam_get_l_aux(b)
-        b[:l_data] - (b[:core][:n_cigar] << 2) - b[:core][:l_qname] - b[:core][:l_qseq] - ((b[:core][:l_qseq] + 1) >> 1)
-      end
-
-      # Get a base on read
-      def bam_seqi(s, i)
-        (s[i >> 1].read_uint8 >> ((~i & 1) << 2)) & 0xf
-      end
-
-      # 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))
-      end
-
-      # Returns the SAM formatted text of the \@HD header line
-      def sam_hdr_find_hd(h, ks)
-        sam_hdr_find_line_id(h, "HD", nil, nil, ks)
-      end
-
-      # Returns the value associated with a given \@HD line tag
-      def sam_hdr_find_tag_hd(h, key, ks)
-        sam_hdr_find_tag_id(h, "HD", nil, nil, key, ks)
-      end
-
-      # Adds or updates tags on the header \@HD line
-      def sam_hdr_update_hd(h, *args)
-        sam_hdr_update_line(h, "HD", nil, nil, *args, nil)
-      end
-
-      # Removes the \@HD line tag with the given key
-      def sam_hdr_remove_tag_hd(h, key)
-        sam_hdr_remove_tag_id(h, "HD", nil, nil, key)
-      end
-
-      BAM_USER_OWNS_STRUCT = 1
-      BAM_USER_OWNS_DATA   = 2
-
-      alias bam_itr_destroy hts_itr_destroy
-      alias bam_itr_queryi sam_itr_queryi
-      alias bam_itr_querys sam_itr_querys
-      alias bam_itr_next sam_itr_next
-
-      # Load/build .csi or .bai BAM index file.  Does not work with CRAM.
-      # It is recommended to use the sam_index_* functions below instead.
-      def bam_index_load(fn)
-        hts_idx_load(fn, HTS_FMT_BAI)
-      end
-
-      alias bam_index_build sam_index_build
-
-      alias sam_itr_destroy hts_itr_destroy
-
-      alias sam_open hts_open
-      alias sam_open_format hts_open_format
-      alias sam_flush hts_flush
-      alias sam_close hts_close
-    end
-  end
-end

data/lib/hts/libhts/tbx.rb

@@ -1,94 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    attach_variable :tbx_conf_gff, TbxConf
-    attach_variable :tbx_conf_bed, TbxConf
-    attach_variable :tbx_conf_psltbl, TbxConf
-    attach_variable :tbx_conf_sam, TbxConf
-    attach_variable :tbx_conf_vcf, TbxConf
-    attach_variable :tbx_conf_gaf, TbxConf
-
-    attach_function \
-      :tbx_name2id,
-      [Tbx, :string],
-      :int
-
-    attach_function \
-      :tbx_itr_querys1,
-      [Tbx, :string],
-      HtsItr.by_ref
-
-    attach_function \
-      :tbx_itr_regarray,
-      [Tbx, :pointer, :uint],
-      HtsItr.by_ref
-
-    attach_function \
-      :tbx_itr_next1,
-      [HtsFile, Tbx, HtsItr, :pointer],
-      :int
-
-    # Internal helper function used by tbx_itr_next()
-    attach_function \
-      :hts_get_bgzfp,
-      [HtsFile],
-      BGZF.by_ref
-
-    attach_function \
-      :tbx_readrec,
-      [BGZF, :pointer, :pointer, :pointer, :pointer, :pointer],
-      :int
-
-    # Build an index of the lines in a BGZF-compressed file
-    attach_function \
-      :tbx_index,
-      [BGZF, :int, TbxConf],
-      Tbx.by_ref
-
-    attach_function \
-      :tbx_index_build,
-      [:string, :int, TbxConf],
-      :int
-
-    attach_function \
-      :tbx_index_build2,
-      [:string, :string, :int, TbxConf],
-      :int
-
-    attach_function \
-      :tbx_index_build3,
-      [:string, :string, :int, :int, TbxConf],
-      :int
-
-    # Load or stream a .tbi or .csi index
-    attach_function \
-      :tbx_index_load,
-      [:string],
-      Tbx.by_ref
-
-    # Load or stream a .tbi or .csi index
-    attach_function \
-      :tbx_index_load2,
-      %i[string string],
-      Tbx.by_ref
-
-    # Load or stream a .tbi or .csi index
-    attach_function \
-      :tbx_index_load3,
-      %i[string string int],
-      Tbx.by_ref
-
-    attach_function \
-      :tbx_seqnames,
-      [Tbx, :pointer],
-      :pointer
-
-    attach_function \
-      :tbx_destroy,
-      [Tbx],
-      :void
-  end
-end
-
-require_relative "tbx_funcs"

data/lib/hts/libhts/tbx_funcs.rb

@@ -1,36 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    class << self
-      def tbx_itr_destroy(iter)
-        hts_itr_destroy(iter)
-      end
-
-      def tbx_itr_queryi(tbx, tid, beg, end_)
-        hts_itr_query(tbx[:idx], tid, beg, end_, @ffi_functions[:tbx_readrec])
-      end
-
-      @@tbx_name2id = proc do |tbx, ss|
-        LibHTS.tbx_name2id(tbx, ss)
-      end
-
-      def tbx_itr_querys(tbx, s)
-        return tbx_itr_querys1(tbx, s) if respond_to?(:tbx_itr_querys1)
-
-        hts_itr_querys(tbx[:idx], s, @@tbx_name2id, tbx, @ffi_functions[:hts_itr_query],
-                       @ffi_functions[:tbx_readrec])
-      end
-
-      def tbx_itr_next(htsfp, tbx, itr, r)
-        return tbx_itr_next1(htsfp, tbx, itr, r) if respond_to?(:tbx_itr_next1)
-
-        hts_itr_next(hts_get_bgzfp(htsfp), itr, r, tbx)
-      end
-
-      def tbx_bgzf_itr_next(bgzfp, tbx, itr, r)
-        hts_itr_next(bgzfp, itr, r, tbx)
-      end
-    end
-  end
-end

data/lib/hts/libhts/thread_pool.rb

@@ -1,139 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    attach_function \
-      :hts_tpool_init,
-      [:int],
-      HtsTpool.by_ref
-
-    attach_function \
-      :hts_tpool_size,
-      [HtsTpool],
-      :int
-
-    # FIXME: struct
-    HtsTpoolProcess = :pointer
-    HtsTpoolResult  = :pointer
-
-    attach_function \
-      :hts_tpool_dispatch,
-      [HtsTpool, HtsTpoolProcess, :pointer, :pointer],
-      :int
-
-    attach_function \
-      :hts_tpool_dispatch2,
-      [HtsTpool, HtsTpoolProcess, :pointer, :pointer, :int],
-      :int
-
-    attach_function \
-      :hts_tpool_dispatch3,
-      [HtsTpool, HtsTpoolProcess, :pointer, :pointer, :pointer, :pointer, :int],
-      :int
-
-    attach_function \
-      :hts_tpool_wake_dispatch,
-      [HtsTpoolProcess],
-      :void
-
-    attach_function \
-      :hts_tpool_process_flush,
-      [HtsTpoolProcess],
-      :int
-
-    attach_function \
-      :hts_tpool_process_reset,
-      [HtsTpoolProcess, :int],
-      :int
-
-    attach_function \
-      :hts_tpool_process_qsize,
-      [HtsTpoolProcess],
-      :int
-
-    attach_function \
-      :hts_tpool_destroy,
-      [HtsTpool],
-      :void
-
-    attach_function \
-      :hts_tpool_kill,
-      [HtsTpool],
-      :void
-
-    attach_function \
-      :hts_tpool_next_result,
-      [HtsTpoolProcess],
-      HtsTpoolResult # .by_ref
-
-    attach_function \
-      :hts_tpool_next_result_wait,
-      [HtsTpoolProcess],
-      HtsTpoolResult # .by_ref
-
-    attach_function \
-      :hts_tpool_delete_result,
-      [HtsTpoolResult, :int],
-      :void
-
-    attach_function \
-      :hts_tpool_result_data,
-      [HtsTpoolResult],
-      :pointer
-
-    attach_function \
-      :hts_tpool_process_init,
-      [HtsTpool, :int, :int],
-      HtsTpoolProcess # .by_ref
-
-    attach_function \
-      :hts_tpool_process_destroy,
-      [HtsTpoolProcess],
-      :void
-
-    attach_function \
-      :hts_tpool_process_empty,
-      [HtsTpoolProcess],
-      :int
-
-    attach_function \
-      :hts_tpool_process_len,
-      [HtsTpoolProcess],
-      :int
-
-    attach_function \
-      :hts_tpool_process_sz,
-      [HtsTpoolProcess],
-      :int
-
-    attach_function \
-      :hts_tpool_process_shutdown,
-      [HtsTpoolProcess],
-      :void
-
-    attach_function \
-      :hts_tpool_process_is_shutdown,
-      [HtsTpoolProcess],
-      :int
-
-    attach_function \
-      :hts_tpool_process_attach,
-      [HtsTpool, HtsTpoolProcess],
-      :void
-
-    attach_function \
-      :hts_tpool_process_detach,
-      [HtsTpool, HtsTpoolProcess],
-      :void
-
-    attach_function \
-      :hts_tpool_process_ref_incr,
-      [HtsTpoolProcess],
-      :void
-
-    attach_function \
-      :hts_tpool_process_ref_decr,
-      [HtsTpoolProcess],
-      :void
-  end
-end