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let colors = let cs = bigarray_create Bigarray . float32 ( 3 * 3 ) in set_3d cs 0 1 . 0 0 . 0 0 . 0 ; set_3d cs 1 0 . 0 1 . 0 0 . 0 ; set_3d cs 2 0 . 0 0 . 0 1 . 0 ; cs |
let indices = let is = bigarray_create Bigarray . int8_unsigned 3 in set_3d is 0 0 1 2 ; is |
let create_buffer b = let id = get_int ( Gl . gen_buffers 1 ) in let bytes = Gl . bigarray_byte_size b in Gl . bind_buffer Gl . array_buffer id ; Gl . buffer_data Gl . array_buffer bytes ( Some b ) Gl . static_draw ; id |
let delete_buffer bid = set_int ( Gl . delete_buffers 1 ) bid |
let create_geometry ( ) = let gid = get_int ( Gl . gen_vertex_arrays 1 ) in let iid = create_buffer indices in let vid = create_buffer vertices in let cid = create_buffer colors in let bind_attrib id loc dim typ = Gl . bind_buffer Gl . array_buffer id ; Gl . enable_vertex_attrib_array loc ; Gl . vertex_attrib_pointer loc dim typ false 0 ( ` Offset 0 ) ; in Gl . bind_vertex_array gid ; Gl . bind_buffer Gl . element_array_buffer iid ; bind_attrib vid 0 3 Gl . float ; bind_attrib cid 1 3 Gl . float ; Gl . bind_vertex_array 0 ; Gl . bind_buffer Gl . array_buffer 0 ; Gl . bind_buffer Gl . element_array_buffer 0 ; Ok ( gid , [ iid ; vid ; cid ] ) |
let delete_geometry gid bids = set_int ( Gl . delete_vertex_arrays 1 ) gid ; List . iter delete_buffer bids ; Ok ( ) |
let compile_shader src typ = let get_shader sid e = get_int ( Gl . get_shaderiv sid e ) in let sid = Gl . create_shader typ in Gl . shader_source sid src ; Gl . compile_shader sid ; if get_shader sid Gl . compile_status = Gl . true_ then Ok sid else let len = get_shader sid Gl . info_log_length in let log = get_string len ( Gl . get_shader_info_log sid len None ) in ( Gl . delete_shader sid ; Error ( ` Msg log ) ) |
let create_program glsl_v = compile_shader ( vertex_shader glsl_v ) Gl . vertex_shader >>= fun vid -> compile_shader ( fragment_shader glsl_v ) Gl . fragment_shader >>= fun fid -> let pid = Gl . create_program ( ) in let get_program pid e = get_int ( Gl . get_programiv pid e ) in Gl . attach_shader pid vid ; Gl . delete_shader vid ; Gl . attach_shader pid fid ; Gl . delete_shader fid ; Gl . bind_attrib_location pid 0 " vertex " ; Gl . bind_attrib_location pid 1 " color " ; Gl . link_program pid ; if get_program pid Gl . link_status = Gl . true_ then Ok pid else let len = get_program pid Gl . info_log_length in let log = get_string len ( Gl . get_program_info_log pid len None ) in ( Gl . delete_program pid ; Error ( ` Msg log ) ) |
let delete_program pid = Gl . delete_program pid ; Ok ( ) |
let draw pid gid win = Gl . clear_color 0 . 0 . 0 . 1 . ; Gl . clear Gl . color_buffer_bit ; Gl . use_program pid ; Gl . bind_vertex_array gid ; Gl . draw_elements Gl . triangles 3 Gl . unsigned_byte ( ` Offset 0 ) ; Gl . bind_vertex_array 0 ; Sdl . gl_swap_window win ; Ok ( ) |
let reshape win w h = Gl . viewport 0 0 w h |
let pp_opengl_info ppf ( ) = let pp = Format . fprintf in let pp_opt ppf = function None -> pp ppf " error " | Some s -> pp ppf " % s " s in pp ppf " [ @< v , " ; >@ pp ppf " Renderer [ @< v [ >@% a ] , " @@ pp_opt ( Gl . get_string Gl . renderer ) ; pp ppf " [ @ OpenGL % a / GLSL % a ] ] , " @@@ pp_opt ( Gl . get_string Gl . version ) pp_opt ( Gl . get_string Gl . shading_language_version ) ; pp ppf " ] " @ |
let create_window ~ gl ( : maj , min ) = let w_atts = Sdl . Window . ( opengl + resizable ) in let w_title = Printf . sprintf " OpenGL % d . % d ( core profile ) " maj min in let set a v = Sdl . gl_set_attribute a v in set Sdl . Gl . context_profile_mask Sdl . Gl . context_profile_core >>= fun ( ) -> set Sdl . Gl . context_major_version maj >>= fun ( ) -> set Sdl . Gl . context_minor_version min >>= fun ( ) -> set Sdl . Gl . doublebuffer 1 >>= fun ( ) -> Sdl . create_window ~ w : 640 ~ h : 480 w_title w_atts >>= fun win -> Sdl . gl_create_context win >>= fun ctx -> Sdl . gl_make_current win ctx >>= fun ( ) -> Sdl . log " % a " pp_opengl_info ( ) ; Ok ( win , ctx ) |
let destroy_window win ctx = Sdl . gl_delete_context ctx ; Sdl . destroy_window win ; Ok ( ) |
let event_loop win draw = let e = Sdl . Event . create ( ) in let key_scancode e = Sdl . Scancode . enum Sdl . Event . ( get e keyboard_scancode ) in let event e = Sdl . Event . ( enum ( get e typ ) ) in let window_event e = Sdl . Event . ( window_event_enum ( get e window_event_id ) ) in let rec loop ( ) = Sdl . wait_event ( Some e ) >>= fun ( ) -> match event e with | ` Quit -> Ok ( ) | ` Key_down when key_scancode e = ` Escape -> Ok ( ) | ` Window_event -> begin match window_event e with | ` Exposed | ` Resized -> let w , h = Sdl . get_window_size win in reshape win w h ; draw win ; draw win ; loop ( ) | _ -> loop ( ) end | _ -> loop ( ) in ( draw win ; loop ( ) ) |
let tri ~ gl ( : maj , min as gl ) = Sdl . init Sdl . Init . video >>= fun ( ) -> create_window ~ gl >>= fun ( win , ctx ) -> create_geometry ( ) >>= fun ( gid , bids ) -> create_program ( glsl_version gl ) >>= fun pid -> event_loop win ( draw pid gid ) >>= fun ( ) -> delete_program pid >>= fun ( ) -> delete_geometry gid bids >>= fun ( ) -> destroy_window win ctx >>= fun ( ) -> Sdl . quit ( ) ; Ok ( ) |
let main ( ) = let exec = Filename . basename Sys . executable_name in let usage = str " Usage : % s [ OPTION ] \ n Tests Tgl4 . \ nOptions " : exec in let minor = ref 0 in let options = [ " - minor " , Arg . Set_int minor , " < x > use Use an OpenGL 4 . x context ( defaults to 4 . 0 ) " ; ] in let anon _ = raise ( Arg . Bad " no arguments are supported " ) in Arg . parse ( Arg . align options ) anon usage ; match tri ~ gl ( : 4 , ! minor ) with | Ok ( ) -> exit 0 | Error ( ` Msg msg ) -> Sdl . log " % s . " @ msg ; exit 1 |
let ( ) = main ( ) |
let ( >>= ) x f = match x with Ok v -> f v | Error _ as e -> e |
let bigarray_create k len = Bigarray . ( Array1 . create k c_layout len ) |
let get_int = let a = bigarray_create Bigarray . int32 1 in fun f -> f a ; Int32 . to_int a . { 0 } |
let set_int = let a = bigarray_create Bigarray . int32 1 in fun f i -> a . { 0 } <- Int32 . of_int i ; f a |
let get_string len f = let a = bigarray_create Bigarray . char len in f a ; Gl . string_of_bigarray a |
let vertex_shader = " # version 100 attribute vec3 vertex ; attribute vec3 color ; varying vec4 v_color ; void main ( ) { v_color = vec4 ( color , 1 . 0 ) ; gl_Position = vec4 ( vertex , 1 . 0 ) ; } " |
let fragment_shader = " # version 100 precision highp float ; varying vec4 v_color ; void main ( ) { gl_FragColor = v_color ; } " |
let set_3d ba i x y z = let start = i * 3 in ba . { start } <- x ; ba . { start + 1 } <- y ; ba . { start + 2 } <- z |
let vertices = let vs = bigarray_create Bigarray . float32 ( 3 * 3 ) in set_3d vs 0 ( - 0 . 8 ) ( - 0 . 8 ) 0 . 0 ; set_3d vs 1 0 . 8 ( - 0 . 8 ) 0 . 0 ; set_3d vs 2 0 . 0 0 . 8 0 . 0 ; vs |
let colors = let cs = bigarray_create Bigarray . float32 ( 3 * 3 ) in set_3d cs 0 1 . 0 0 . 0 0 . 0 ; set_3d cs 1 0 . 0 1 . 0 0 . 0 ; set_3d cs 2 0 . 0 0 . 0 1 . 0 ; cs |
let indices = let is = bigarray_create Bigarray . int8_unsigned 3 in set_3d is 0 0 1 2 ; is |
let create_buffer b = let id = get_int ( Gl . gen_buffers 1 ) in let bytes = Gl . bigarray_byte_size b in Gl . bind_buffer Gl . array_buffer id ; Gl . buffer_data Gl . array_buffer bytes ( Some b ) Gl . static_draw ; id |
let delete_buffer bid = set_int ( Gl . delete_buffers 1 ) bid |
let create_geometry ( ) = let iid = create_buffer indices in let vid = create_buffer vertices in let cid = create_buffer colors in Ok ( iid , vid , cid ) |
let delete_geometry ( iid , vid , cid ) = delete_buffer iid ; delete_buffer vid ; delete_buffer cid ; Ok ( ) |
let compile_shader src typ = let get_shader sid e = get_int ( Gl . get_shaderiv sid e ) in let sid = Gl . create_shader typ in Gl . shader_source sid src ; Gl . compile_shader sid ; if get_shader sid Gl . compile_status = Gl . true_ then Ok sid else let len = get_shader sid Gl . info_log_length in let log = get_string len ( Gl . get_shader_info_log sid len None ) in ( Gl . delete_shader sid ; Error ( ` Msg log ) ) |
let create_program ( ) = compile_shader vertex_shader Gl . vertex_shader >>= fun vid -> compile_shader fragment_shader Gl . fragment_shader >>= fun fid -> let pid = Gl . create_program ( ) in let get_program pid e = get_int ( Gl . get_programiv pid e ) in Gl . attach_shader pid vid ; Gl . delete_shader vid ; Gl . attach_shader pid fid ; Gl . delete_shader fid ; Gl . bind_attrib_location pid 0 " vertex " ; Gl . bind_attrib_location pid 1 " color " ; Gl . link_program pid ; if get_program pid Gl . link_status = Gl . true_ then Ok pid else let len = get_program pid Gl . info_log_length in let log = get_string len ( Gl . get_program_info_log pid len None ) in ( Gl . delete_program pid ; Error ( ` Msg log ) ) |
let delete_program pid = Gl . delete_program pid ; Ok ( ) |
let draw pid ( iid , vid , cid ) win = let bind_attrib id loc dim typ = Gl . bind_buffer Gl . array_buffer id ; Gl . enable_vertex_attrib_array loc ; Gl . vertex_attrib_pointer loc dim typ false 0 ( ` Offset 0 ) ; in Gl . clear_color 0 . 0 . 0 . 1 . ; Gl . clear Gl . color_buffer_bit ; Gl . use_program pid ; Gl . bind_buffer Gl . element_array_buffer iid ; bind_attrib vid 0 3 Gl . float ; bind_attrib cid 1 3 Gl . float ; Gl . draw_elements Gl . triangles 3 Gl . unsigned_byte ( ` Offset 0 ) ; Gl . bind_buffer Gl . array_buffer 0 ; Gl . bind_buffer Gl . element_array_buffer 0 ; Sdl . gl_swap_window win ; Ok ( ) |
let reshape win w h = Gl . viewport 0 0 w h |
let pp_opengl_info ppf ( ) = let pp = Format . fprintf in let pp_opt ppf = function None -> pp ppf " error " | Some s -> pp ppf " % s " s in pp ppf " [ @< v , " ; >@ pp ppf " Renderer [ @< v [ >@% a ] , " @@ pp_opt ( Gl . get_string Gl . renderer ) ; pp ppf " [ @ OpenGL % a / GLSL % a ] ] , " @@@ pp_opt ( Gl . get_string Gl . version ) pp_opt ( Gl . get_string Gl . shading_language_version ) ; pp ppf " ] " @ |
let create_window ~ gl ( : maj , min ) = let w_atts = Sdl . Window . ( opengl + resizable ) in let w_title = Printf . sprintf " OpenGL % d . % d ( core profile ) " maj min in let set a v = Sdl . gl_set_attribute a v in set Sdl . Gl . context_profile_mask Sdl . Gl . context_profile_es >>= fun ( ) -> set Sdl . Gl . context_major_version maj >>= fun ( ) -> set Sdl . Gl . context_minor_version min >>= fun ( ) -> set Sdl . Gl . doublebuffer 1 >>= fun ( ) -> Sdl . create_window ~ w : 640 ~ h : 480 w_title w_atts >>= fun win -> Sdl . gl_create_context win >>= fun ctx -> Sdl . gl_make_current win ctx >>= fun ( ) -> Sdl . log " % a " pp_opengl_info ( ) ; Ok ( win , ctx ) |
let destroy_window win ctx = Sdl . gl_delete_context ctx ; Sdl . destroy_window win ; Ok ( ) |
let event_loop win draw = let e = Sdl . Event . create ( ) in let key_scancode e = Sdl . Scancode . enum Sdl . Event . ( get e keyboard_scancode ) in let event e = Sdl . Event . ( enum ( get e typ ) ) in let window_event e = Sdl . Event . ( window_event_enum ( get e window_event_id ) ) in let rec loop ( ) = Sdl . wait_event ( Some e ) >>= fun ( ) -> match event e with | ` Quit -> Ok ( ) | ` Key_down when key_scancode e = ` Escape -> Ok ( ) | ` Window_event -> begin match window_event e with | ` Exposed | ` Resized -> let w , h = Sdl . get_window_size win in reshape win w h ; draw win ; loop ( ) | _ -> loop ( ) end | _ -> loop ( ) in ( draw win ; loop ( ) ) |
let tri ~ gl ( : maj , min as gl ) = Sdl . init Sdl . Init . video >>= fun ( ) -> create_window ~ gl >>= fun ( win , ctx ) -> create_geometry ( ) >>= fun bids -> create_program ( ) >>= fun pid -> event_loop win ( draw pid bids ) >>= fun ( ) -> delete_program pid >>= fun ( ) -> delete_geometry bids >>= fun ( ) -> destroy_window win ctx >>= fun ( ) -> Sdl . quit ( ) ; Ok ( ) |
let main ( ) = let exec = Filename . basename Sys . executable_name in let usage = str " Usage : % s [ OPTION ] \ n Tests Tgles2 . \ nOptions " : exec in let options = [ ] in let anon _ = raise ( Arg . Bad " no arguments are supported " ) in Arg . parse ( Arg . align options ) anon usage ; match tri ~ gl ( : 2 , 0 ) with | Ok ( ) -> exit 0 | Error ( ` Msg msg ) -> Sdl . log " % s . " @ msg ; exit 1 |
let ( ) = main ( ) |
let ( >>= ) x f = match x with Ok v -> f v | Error _ as e -> e |
let bigarray_create k len = Bigarray . ( Array1 . create k c_layout len ) |
let get_int = let a = bigarray_create Bigarray . int32 1 in fun f -> f a ; Int32 . to_int a . { 0 } |
let set_int = let a = bigarray_create Bigarray . int32 1 in fun f i -> a . { 0 } <- Int32 . of_int i ; f a |
let get_string len f = let a = bigarray_create Bigarray . char len in f a ; Gl . string_of_bigarray a |
let vertex_shader = " # version 330 es in vec3 vertex ; in vec3 color ; out vec4 v_color ; void main ( ) { v_color = vec4 ( color , 1 . 0 ) ; gl_Position = vec4 ( vertex , 1 . 0 ) ; } " |
let fragment_shader = " # version 330 es precision highp float ; in vec4 v_color ; out vec4 color ; void main ( ) { color = v_color ; } " |
let set_3d ba i x y z = let start = i * 3 in ba . { start } <- x ; ba . { start + 1 } <- y ; ba . { start + 2 } <- z |
let vertices = let vs = bigarray_create Bigarray . float32 ( 3 * 3 ) in set_3d vs 0 ( - 0 . 8 ) ( - 0 . 8 ) 0 . 0 ; set_3d vs 1 0 . 8 ( - 0 . 8 ) 0 . 0 ; set_3d vs 2 0 . 0 0 . 8 0 . 0 ; vs |
let colors = let cs = bigarray_create Bigarray . float32 ( 3 * 3 ) in set_3d cs 0 1 . 0 0 . 0 0 . 0 ; set_3d cs 1 0 . 0 1 . 0 0 . 0 ; set_3d cs 2 0 . 0 0 . 0 1 . 0 ; cs |
let indices = let is = bigarray_create Bigarray . int8_unsigned 3 in set_3d is 0 0 1 2 ; is |
let create_buffer b = let id = get_int ( Gl . gen_buffers 1 ) in let bytes = Gl . bigarray_byte_size b in Gl . bind_buffer Gl . array_buffer id ; Gl . buffer_data Gl . array_buffer bytes ( Some b ) Gl . static_draw ; id |
let delete_buffer bid = set_int ( Gl . delete_buffers 1 ) bid |
let create_geometry ( ) = let gid = get_int ( Gl . gen_vertex_arrays 1 ) in let iid = create_buffer indices in let vid = create_buffer vertices in let cid = create_buffer colors in let bind_attrib id loc dim typ = Gl . bind_buffer Gl . array_buffer id ; Gl . enable_vertex_attrib_array loc ; Gl . vertex_attrib_pointer loc dim typ false 0 ( ` Offset 0 ) ; in Gl . bind_vertex_array gid ; Gl . bind_buffer Gl . element_array_buffer iid ; bind_attrib vid 0 3 Gl . float ; bind_attrib cid 1 3 Gl . float ; Gl . bind_vertex_array 0 ; Gl . bind_buffer Gl . array_buffer 0 ; Gl . bind_buffer Gl . element_array_buffer 0 ; Ok ( gid , [ iid ; vid ; cid ] ) |
let delete_geometry gid bids = set_int ( Gl . delete_vertex_arrays 1 ) gid ; List . iter delete_buffer bids ; Ok ( ) |
let compile_shader src typ = let get_shader sid e = get_int ( Gl . get_shaderiv sid e ) in let sid = Gl . create_shader typ in Gl . shader_source sid src ; Gl . compile_shader sid ; if get_shader sid Gl . compile_status = Gl . true_ then Ok sid else let len = get_shader sid Gl . info_log_length in let log = get_string len ( Gl . get_shader_info_log sid len None ) in ( Gl . delete_shader sid ; Error ( ` Msg log ) ) |
let create_program ( ) = compile_shader vertex_shader Gl . vertex_shader >>= fun vid -> compile_shader fragment_shader Gl . fragment_shader >>= fun fid -> let pid = Gl . create_program ( ) in let get_program pid e = get_int ( Gl . get_programiv pid e ) in Gl . attach_shader pid vid ; Gl . delete_shader vid ; Gl . attach_shader pid fid ; Gl . delete_shader fid ; Gl . bind_attrib_location pid 0 " vertex " ; Gl . bind_attrib_location pid 1 " color " ; Gl . link_program pid ; if get_program pid Gl . link_status = Gl . true_ then Ok pid else let len = get_program pid Gl . info_log_length in let log = get_string len ( Gl . get_program_info_log pid len None ) in ( Gl . delete_program pid ; Error ( ` Msg log ) ) |
let delete_program pid = Gl . delete_program pid ; Ok ( ) |
let draw pid gid win = Gl . clear_color 0 . 0 . 0 . 1 . ; Gl . clear Gl . color_buffer_bit ; Gl . use_program pid ; Gl . bind_vertex_array gid ; Gl . draw_elements Gl . triangles 3 Gl . unsigned_byte ( ` Offset 0 ) ; Gl . bind_vertex_array 0 ; Sdl . gl_swap_window win ; Ok ( ) |
let reshape win w h = Gl . viewport 0 0 w h |
let pp_opengl_info ppf ( ) = let pp = Format . fprintf in let pp_opt ppf = function None -> pp ppf " error " | Some s -> pp ppf " % s " s in pp ppf " [ @< v , " ; >@ pp ppf " Renderer [ @< v [ >@% a ] , " @@ pp_opt ( Gl . get_string Gl . renderer ) ; pp ppf " [ @ OpenGL % a / GLSL % a ] ] , " @@@ pp_opt ( Gl . get_string Gl . version ) pp_opt ( Gl . get_string Gl . shading_language_version ) ; pp ppf " ] " @ |
let create_window ~ gl ( : maj , min ) = let w_atts = Sdl . Window . ( opengl + resizable ) in let w_title = Printf . sprintf " OpenGL % d . % d ( core profile ) " maj min in let set a v = Sdl . gl_set_attribute a v in set Sdl . Gl . context_profile_mask Sdl . Gl . context_profile_es >>= fun ( ) -> set Sdl . Gl . context_major_version maj >>= fun ( ) -> set Sdl . Gl . context_minor_version min >>= fun ( ) -> set Sdl . Gl . doublebuffer 1 >>= fun ( ) -> Sdl . create_window ~ w : 640 ~ h : 480 w_title w_atts >>= fun win -> Sdl . gl_create_context win >>= fun ctx -> Sdl . gl_make_current win ctx >>= fun ( ) -> Sdl . log " % a " pp_opengl_info ( ) ; Ok ( win , ctx ) |
let destroy_window win ctx = Sdl . gl_delete_context ctx ; Sdl . destroy_window win ; Ok ( ) |
let event_loop win draw = let e = Sdl . Event . create ( ) in let key_scancode e = Sdl . Scancode . enum Sdl . Event . ( get e keyboard_scancode ) in let event e = Sdl . Event . ( enum ( get e typ ) ) in let window_event e = Sdl . Event . ( window_event_enum ( get e window_event_id ) ) in let rec loop ( ) = Sdl . wait_event ( Some e ) >>= fun ( ) -> match event e with | ` Quit -> Ok ( ) | ` Key_down when key_scancode e = ` Escape -> Ok ( ) | ` Window_event -> begin match window_event e with | ` Exposed | ` Resized -> let w , h = Sdl . get_window_size win in reshape win w h ; draw win ; draw win ; loop ( ) | _ -> loop ( ) end | _ -> loop ( ) in ( draw win ; loop ( ) ) |
let tri ~ gl ( : maj , min as gl ) = Sdl . init Sdl . Init . video >>= fun ( ) -> create_window ~ gl >>= fun ( win , ctx ) -> create_geometry ( ) >>= fun ( gid , bids ) -> create_program ( ) >>= fun pid -> event_loop win ( draw pid gid ) >>= fun ( ) -> delete_program pid >>= fun ( ) -> delete_geometry gid bids >>= fun ( ) -> destroy_window win ctx >>= fun ( ) -> Sdl . quit ( ) ; Ok ( ) |
let main ( ) = let exec = Filename . basename Sys . executable_name in let usage = str " Usage : % s [ OPTION ] \ n Tests Tgles3 . \ nOptions " : exec in let options = [ ] in let anon _ = raise ( Arg . Bad " no arguments are supported " ) in Arg . parse ( Arg . align options ) anon usage ; match tri ~ gl ( : 3 , 0 ) with | Ok ( ) -> exit 0 | Error ( ` Msg msg ) -> Sdl . log " % s . " @ msg ; exit 1 |
let ( ) = main ( ) |
module Trimming_result = struct type t = { trimmed_bytes : int64 } let empty = { trimmed_bytes = 0L } let add t ( ~ bytes : int ) = { trimmed_bytes = Int64 . add t . trimmed_bytes ( Int64 . of_int bytes ) } end |
let trim_broken_metadata_entries ~ trimmed_so_far = List . fold_left Version . Metadata . all ~ init : trimmed_so_far ~ f ( : fun trimmed_so_far version -> let metadata_entries = Layout . Versioned . list_metadata_entries version in let file_path = Layout . Versioned . file_path ( Version . Metadata . file_version version ) in List . fold_left metadata_entries ~ init : trimmed_so_far ~ f ( : fun trimmed_so_far ( path , rule_or_action_digest ) -> let should_be_removed = match Metadata . Versioned . restore version ~ rule_or_action_digest with | Not_found_in_cache -> false | Error _exn -> true | Restored metadata -> ( match metadata with | Metadata . Value _ -> false | Metadata . Artifacts { entries ; _ } -> List . exists entries ~ f ( : fun { Artifacts . Metadata_entry . file_digest ; _ } -> let reference = file_path ~ file_digest in not ( Path . exists reference ) ) ) in match should_be_removed with | true -> ( match Path . stat path with | Ok stats -> let bytes = stats . st_size in Path . unlink_no_err path ; Trimming_result . add trimmed_so_far ~ bytes | Error _ -> trimmed_so_far ) | false -> trimmed_so_far ) ) |
let garbage_collect ( ) = trim_broken_metadata_entries ~ trimmed_so_far : Trimming_result . empty |
let files_in_cache_for_all_supported_versions ( ) = List . concat_map Version . File . all ~ f ( : fun file_version -> Layout . Versioned . list_file_entries file_version ) |
let file_exists_and_is_unused ~ stats = stats . Unix . st_nlink = 1 |
let trim ~ goal = let files = files_in_cache_for_all_supported_versions ( ) |> List . map ~ f : fst in let files = List . sort ~ compare ( : fun ( _ , _ , ctime1 ) ( _ , _ , ctime2 ) -> Poly . compare ctime1 ctime2 ) ( List . filter_map files ~ f ( : fun path -> match Path . stat path with | Ok stats -> if file_exists_and_is_unused ~ stats then Some ( path , stats . st_size , stats . st_ctime ) else None | Error _ -> None ) ) in let delete ( trimmed_so_far : Trimming_result . t ) ( path , bytes , _ ) = if trimmed_so_far . trimmed_bytes >= goal then trimmed_so_far else ( Path . unlink_no_err path ; Trimming_result . add trimmed_so_far ~ bytes ) in let trimmed_so_far = List . fold_left ~ init : Trimming_result . empty ~ f : delete files in trim_broken_metadata_entries ~ trimmed_so_far |
let overhead_size ( ) = let files = files_in_cache_for_all_supported_versions ( ) |> List . map ~ f : fst in let stats = let f p = try let stats = Path . stat_exn p in if file_exists_and_is_unused ~ stats then Int64 . of_int stats . st_size else 0L with Unix . Unix_error ( Unix . ENOENT , _ , _ ) -> 0L in List . map ~ f files in List . fold_left ~ f : Int64 . add ~ init : 0L stats |
let img = [ docker_image ~ account " : pveber " ~ name " : trinity " ~ tag " : 2 . 9 . 1 " ( ) ] |
let fqs_option_template fastq_samples = let ( fqs , fq1s , fq2s ) , ( fq_gzs , fq1_gzs , fq2_gzs ) = Fastq_sample . explode fastq_samples in let arg_list plain_files compressed_files = let tokens = List . map plain_files ~ f : dep @ List . map compressed_files ~ f : Bistro_unix . Cmd . gzdep in match tokens with | [ ] -> None | _ :: _ -> Some ( seq ~ sep " , " : tokens ) in let maybe_opt o = Option . map ~ f ( : opt o Fn . id ) in [ maybe_opt " -- single " ( arg_list fqs fq_gzs ) ; maybe_opt " -- left " ( arg_list fq1s fq1_gzs ) ; maybe_opt " -- right " ( arg_list fq2s fq2_gzs ) ; ] |> List . filter_opt |> seq ~ sep " : " |
let ss_lib_type_option o = opt " -- SS_lib_type " string ( match o with | ` R -> " R " | ` F -> " F " | ` RF -> " RF " | ` FR -> " FR " ) |
let trinity ( ? mem = 128 ) ( ? threads = 4 ) ? no_normalize_reads ? run_as_paired ? min_kmer_cov ? ss_lib_type se_or_pe_fq = let tmp_dest = tmp // " trinity " in Workflow . shell ~ descr " : trinity " ~ img ~ np : threads ~ mem ( : Workflow . int ( mem * 1024 ) ) [ mkdir_p tmp ; cmd " Trinity " ~ stdout ( : string " / dev / null " ) [ string " -- seqType fq " ; fqs_option_template se_or_pe_fq ; option ( flag string " -- no_normalize_reads " ) no_normalize_reads ; option ( flag string " -- run_as_paired " ) run_as_paired ; option ( opt " -- min_kmer_cov " int ) min_kmer_cov ; option ss_lib_type_option ss_lib_type ; opt " -- CPU " Fun . id np ; opt " -- max_memory " Fun . id ( seq [ string " ( ( " $ ; Bistro . Shell_dsl . mem ; string " / 1024 ) ) G " ] ) ; opt " -- output " Fun . id tmp_dest ; ] ; cmd " mv " [ tmp_dest // " Trinity . fasta " ; dest ; ] ] |
let prepare_fastq n fq = Workflow . shell ~ descr " : trinity . prepare_fastq " [ pipe [ cmd " zcat " [ dep fq ] ; cmd " awk " ~ stdout : dest [ sprintf { ' { | if ( NR %% 4 == 1 && ( !$ 1 ~ . /*\/% d ) ) / { print $ 1 " /% d " } else { print } } ' } | n n |> string ] ; ] ] |
let uniq_count_stats sam = let sorted_sam = sam |> Samtools . bam_of_sam |> Samtools . sort ~ on ` : name in Workflow . shell ~ descr " : trinity . uniq_count_stats . pl " ~ img [ cmd " $ TRINITY_HOME / util / SAM_nameSorted_to_uniq_count_stats . pl " ~ stdout : dest [ dep sorted_sam ; ] ] |
let fq_option_template = function | SE_or_PE . Single_end fqs -> opt " -- single " dep fqs | Paired_end ( fqs1 , fqs2 ) -> seq ~ sep " : " [ opt " -- left " dep fqs1 ; opt " -- right " dep fqs2 ; ] |
let bash_app f x = seq ~ sep " " : ( string " ( " $ :: string f :: string " " :: x @ [ string " ) " ] ) |
let insilico_read_normalization ( ? mem = 128 ) ? pairs_together ? parallel_stats ~ max_cov se_or_pe_fq = let trinity_cmd = cmd " $ TRINITY_HOME / util / insilico_read_normalization . pl " [ string " -- seqType fq " ; fq_option_template se_or_pe_fq ; opt " -- CPU " Fun . id np ; opt " -- JM " Fun . id ( seq [ string " ( ( " $ ; Bistro . Shell_dsl . mem ; string " / 1024 ) ) G " ] ) ; opt " -- max_cov " int max_cov ; option ( flag string " -- pairs_together " ) pairs_together ; option ( flag string " -- PARALLEL_STATS " ) parallel_stats ; opt " -- output " Fun . id tmp ; ] in let workflow post = Workflow . shell ~ descr " : trinity . insilico_read_normalization " ~ np : 32 ~ mem ( : Workflow . int ( mem * 1024 ) ) ~ img ( trinity_cmd :: post ) in let mv x y = mv ( bash_app " readlink " [ tmp // x ] ) y in match se_or_pe_fq with | Single_end _ -> SE_or_PE . Single_end ( workflow [ mv " single . norm . fq " dest ] ) | Paired_end _ -> let post = [ mkdir_p dest ; mv " left . norm . fq " ( dest // " left . fq " ) ; mv " right . norm . fq " ( dest // " right . fq " ) ; ] in let inner = workflow post in Paired_end ( Workflow . select inner [ " left . fq " ] , Workflow . select inner [ " right . fq " ] ) |
let get_Trinity_gene_to_trans_map fa = Workflow . shell ~ descr " : get_Trinity_gene_to_trans_map " ~ img [ cmd " $ TRINITY_HOME / util / support_scripts / get_Trinity_gene_to_trans_map . pl " ~ stdout : dest [ dep fa ] ] |
type cursor = O . t include ( struct type ' + a cell = { offset : int ; cursor : cursor ; value : ' a } let make_cell offset cursor value = assert ( offset >= 0 ) ; { offset ; cursor ; value } let shift_cell n c = if n = 0 then c else make_cell ( c . offset + n ) c . cursor c . value end : sig type ' + a cell = private { offset : int ; cursor : cursor ; value : ' a } val make_cell : int -> cursor -> ' a -> ' a cell val shift_cell : int -> ' a cell -> ' a cell end ) |
module T = Mbt . Make ( struct type ' a measurable = ' a cell type measure = int let empty = 0 let cat a b c = a + b . offset + c end ) |
type ' a t = { root : O . t ; tree : ' a T . t ; } |
let create ( ) = { root = O . root ( ) ; tree = T . leaf ; } |
let validate t c msg = if not ( O . same_order t . root c ) then invalid_arg msg |
let update t f = let tree , result = f t . tree in { t with tree } , result |
let update ' t f = { t with tree = f t . tree } |
let clear t = { t with tree = T . leaf } |
let is_leaf = function | T . Leaf -> true | T . Node _ -> false |
let is_empty t = is_leaf t . tree |
let member t c = let rec aux = function | T . Leaf -> false | T . Node ( _ , l , cell , r , _ ) -> let o = compare c cell . cursor in if o = 0 then true else if o < 0 then aux l else aux r in aux t . tree |
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