ruby-igv 0.0.9 → 0.0.10

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@@ -1,7 +1,7 @@
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data/README.md

@@ -12,12 +12,12 @@ Ruby-IGV is a simple tool for controlling the Integrated Genomics Viewer (IGV) f
 
 <img src="https://user-images.githubusercontent.com/5798442/182540876-c3ca2906-7d05-4c93-9107-ce4135ae9765.png" width="300" align="right">
 
-Requirement : 
+Requirement :
 
-* [Ruby](https://github.com/ruby/ruby)
-* [IGV (Integrative Genomics Viewer)](http://software.broadinstitute.org/software/igv/)
-  * [Enable IGV to listen on the port](https://software.broadinstitute.org/software/igv/Preferences#Advanced)
-  * View > Preference > Advanced > Enable port ☑
+- [Ruby](https://github.com/ruby/ruby)
+- [IGV (Integrative Genomics Viewer)](http://software.broadinstitute.org/software/igv/)
+  - [Enable IGV to listen on the port](https://software.broadinstitute.org/software/igv/Preferences#Advanced)
+  - View > Preference > Advanced > Enable port ☑
 
 ```ruby
 gem install ruby-igv
@@ -45,7 +45,7 @@ igv.snapshot 'region.png'
 
 ### IGV batch commands
 
-The commonly used commands in IGV are summarized in the official [list of batch commands](https://github.com/igvteam/igv/wiki/Batch-commands). (but even this does not seem to be all of them). You can also call the `commands` method from Ruby to open a browser and view the list.
+The commonly used commands in IGV are summarized in the official [list of batch commands](https://igv.org/doc/desktop/#UserGuide/tools/batch/#script-commands). (but even this does not seem to be all of them). You can also call the `commands` method from Ruby to open a browser and view the list.
 
 ```ruby
 igv.commands # Show the IGV command reference in your browser
@@ -53,18 +53,35 @@ igv.commands # Show the IGV command reference in your browser
 
 ### docs
 
-See [yard docs](https://rubydoc.info/gems/ruby-igv/IGV). Commonly used IGV batch commands can be called from Ruby methods of the same name. However, not all IGV batch commands are implemented in Ruby. Use the `send` method described below.
+See [yard docs](https://kojix2.github.io/ruby-igv/).  
+Most IGV batch commands are available as Ruby methods of the same name.  
+If you need to use a command not directly wrapped, you can use the `send` method as shown below.
 
 ### send
 
-Commands that are not implemented can be sent using the send method.
+You can send any IGV batch command using the `send` method.
 
 ```ruby
 igv.send("maxPanelHeight", 10)
+igv.send("scrollToTop")
+igv.send("setAccessToken", "token", "host")
 ```
 
 To avoid unexpected behavior, ruby-igv does not use the `method_missing` mechanism.
 
+### Supported IGV batch commands
+
+Most official IGV batch commands are available as Ruby methods, including:
+
+- collapse, color_by, echo, exit, expand, genome, goto, group, load, max_panel_height, new, overlay, preference, region, save_session, scroll_to_top, separate, set_alt_color, set_color, set_data_range, set_log_scale, set_sequence_strand, set_sequence_show_translation, set_sleep_interval, set_track_height, snapshot_dir, snapshot, sort, squish, viewaspairs, set_access_token, clear_access_tokens
+
+See the [official IGV batch command list](https://igv.org/doc/desktop/#UserGuide/tools/batch/#script-commands) for details.
+
+### Return values and error handling
+
+Most methods return the IGV response string (e.g. "OK" or an error message).  
+You can check the return value to handle errors or confirm success.
+
 ### Launch IGV
 
 Launch IGV from Ruby script.
@@ -121,10 +138,10 @@ igv.kill        # kill group pid created with IGV.start
 
 ## Contributing
 
-* [Report bugs](https://github.com/kojix2/ruby-igv/issues)
-* Fix bugs and submit [pull requests](https://github.com/kojix2/ruby-igv/pulls)
-* Write, clarify, or fix documentation
-* Suggest or add new features
+- [Report bugs](https://github.com/kojix2/ruby-igv/issues)
+- Fix bugs and submit [pull requests](https://github.com/kojix2/ruby-igv/pulls)
+- Write, clarify, or fix documentation
+- Suggest or add new features
 
 ```
 Do you need commit rights to this repository?
@@ -133,8 +150,10 @@ If so, please feel free to contact me @kojix2.
 ```
 
 ## Acknowledgement
+
 This gem is strongly inspired by a Python script developed by Brent Pedersen.
-* [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
+
+- [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
 
 ## License
 

data/lib/igv/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 class IGV
-  VERSION = '0.0.9'
+  VERSION = '0.0.10'
 end

data/lib/igv.rb

@@ -5,20 +5,21 @@ require 'uri'
 require 'socket'
 require 'fileutils'
 
-# The Integrative Genomics Viewer (IGV)
-# https://software.broadinstitute.org/software/igv/
+# The Integrative Genomics Viewer (IGV) Ruby client.
+# Provides a Ruby interface to control IGV via its batch command protocol.
+#
+# @see https://igv.org/doc/desktop/#UserGuide/tools/batch/#script-commands IGV Batch Script Documentation
 class IGV
   class Error < StandardError; end
 
   attr_reader :host, :port, :history
 
-  # Create IGV client object
+  # Create IGV client object.
   #
-  # @param host [String] hostname or IP address of IGV server
-  # @param port [Integer] port number of IGV server
-  # @param path [String] directory path to save snapshots
-  # @return [IGV] IGV client object
-
+  # @param host [String] Hostname or IP address of IGV server.
+  # @param port [Integer] Port number of IGV server.
+  # @param snapshot_dir [String] Directory path to save snapshots.
+  # @return [IGV] IGV client object.
   def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
     raise ArgumentError, 'IGV#initialize does not accept a block.' if block_given?
 
@@ -28,15 +29,14 @@ class IGV
     @history = []
   end
 
-  # Create IGV object and connect to IGV server
+  # Create IGV object and connect to IGV server.
   # This method accepts a block.
   #
-  # @param host [String] hostname or IP address of IGV server
-  # @param port [Integer] port number of IGV server
-  # @param path [String] directory path to save snapshots
-  # @return [IGV] IGV client object
-  # @yield [IGV] IGV client object
-
+  # @param host [String] Hostname or IP address of IGV server.
+  # @param port [Integer] Port number of IGV server.
+  # @param snapshot_dir [String] Directory path to save snapshots.
+  # @yield [IGV] IGV client object.
+  # @return [IGV] IGV client object.
   def self.open(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
     igv = new(host: host, port: port, snapshot_dir: snapshot_dir)
     igv.connect
@@ -50,23 +50,26 @@ class IGV
     igv
   end
 
+  # Check if a port is open.
+  # @param port [Integer] Port number.
+  # @return [Boolean, nil] true if open, false if closed, nil if unknown.
   def self.port_open?(port)
     system("lsof -i:#{port}", out: '/dev/null')
   end
   private_class_method :port_open?
 
-  # Launch IGV from ruby script
+  # Launch IGV from Ruby script.
   #
-  # @param port [Integer] port number
-  # @param command [String] command to launch IGV
-  # @param snapshot_dir [String] directory path to save snapshots
-  # @return [IGV] IGV client object
-
+  # @param port [Integer] Port number.
+  # @param command [String] Command to launch IGV.
+  # @param snapshot_dir [String] Directory path to save snapshots.
+  # @return [IGV] IGV client object.
+  # @note This will spawn a new IGV process and connect to it.
   def self.start(port: 60_151, command: 'igv', snapshot_dir: Dir.pwd)
     case port_open?(port)
-    when nil   then warn "Cannot tell if port #{port} is open"
+    when nil   then warn "[ruby-igv] Cannot tell if port #{port} is open"
     when true  then raise("Port #{port} is already in use")
-    when false then warn "Port #{port} is available"
+    when false then warn "[ruby-igv] Port #{port} is available"
     else raise "Unexpected return value from port_open?(#{port})"
     end
     r, w = IO.pipe
@@ -84,38 +87,44 @@ class IGV
     igv
   end
 
-  # Kill IGV process by process group id
-
+  # Kill IGV process by process group id.
+  #
+  # @note Only works for IGV processes started by IGV.start.
+  # @return [nil] Kills the IGV process if started by this client, otherwise does nothing.
   def kill
     if instance_variable_defined?(:@pgid_igv)
-      warn \
-        'This method kills the process with the group ID specified at startup. ' \
-        'Please use exit or quit if possible.'
+      warn '[ruby-igv] This method kills the process with the group ID specified at startup. Please use exit or quit if possible.'
     else
-      warn \
-        'The kill method terminates only IGV commands invoked by the start method.' \
-        'Otherwise, use exit or quit.'
-      return
+      warn '[ruby-igv] The kill method terminates only IGV commands invoked by the start method. Otherwise, use exit or quit.'
+      return nil
     end
     pgid = @pgid_igv
     Process.kill(:TERM, -pgid)
     close
+    nil
   end
 
-  # Connect to IGV server
-
+  # Connect to IGV server.
+  #
+  # @param host2 [String] Hostname or IP address.
+  # @param port2 [Integer] Port number.
+  # @param connect_timeout [Integer, nil] Timeout in seconds.
+  # @return [self] Returns self for method chaining.
   def connect(host2 = @host, port2 = @port, connect_timeout: nil)
     @socket&.close
     @socket = Socket.tcp(host2, port2, connect_timeout: connect_timeout)
+    self
   end
 
-  # Close the socket.
-  # This method dose not exit IGV.
-
+  # Close the socket. This does not exit IGV.
+  # @return [nil] Closes the socket and returns nil.
   def close
     @socket&.close
+    nil
   end
 
+  # Check if the socket is closed.
+  # @return [Boolean]
   def closed?
     return true if @socket.nil?
 
@@ -124,9 +133,10 @@ class IGV
 
   # Send batch commands to IGV.
   #
-  # @param *cmds [String, Symbol, Numeric] batch commands
-  # @return [String] response from IGV
-
+  # @param cmds [Array<String, Symbol, Numeric>] Batch commands.
+  # @return [String] Response from IGV.
+  # @example
+  #   igv.send("goto", "chr1:1000-2000")
   def send(*cmds)
     cmd = \
       cmds
@@ -146,40 +156,42 @@ class IGV
 
   # Syntactic sugar for IGV commands that begin with set.
   #
+  # @param cmd [String, Symbol] Batch command name (without "set" prefix).
+  # @param params [Array<String, Symbol, Numeric>] Parameters for the command.
+  # @return [String] Response from IGV.
   # @example
   #   igv.set :SleepInterval, 100
   #   igv.send "setSleepInterval", 100 # same as above
-  # @param cmd [String, Symbol] batch commands
-  # @param *params [String, Symbol, Numeric] batch commands
-
   def set(cmd, *params)
     cmd = "set#{cmd}"
     send(cmd, *params)
   end
 
-  # Show IGV batch commands in the browser.
-  # https://github.com/igvteam/igv/wiki/Batch-commands
-
+  # Open IGV batch command documentation in the browser.
   def commands
     require 'launchy'
-    Launchy.open('https://github.com/igvteam/igv/wiki/Batch-commands')
+    Launchy.open('https://igv.org/doc/desktop/#UserGuide/tools/batch/#script-commands')
   end
 
-  # Writes the value of "param" back to the response
-  # @note IGV Batch command
+  # Write the value of "param" back to the response.
   #
-  # @param param [String] The parameter to echo.
+  # @note IGV Batch command: echo
+  # @param param [String, nil] The parameter to echo.
   # @return [String] The value of "param". If param is not specified, "echo".
-
+  # @example
+  #   igv.echo("Hello!") #=> "Hello!"
   def echo(param = nil)
     send :echo, param
   end
 
-  # Selects a genome by id, or loads a genome (or indexed fasta) from the supplied path.
-  # @note IGV Batch command
+  # Select a genome by id, or load a genome (or indexed fasta) from the supplied path.
   #
-  # @param name_or_path [String] The genome to load
-
+  # @note IGV Batch command: genome
+  # @param name_or_path [String] Genome id (e.g. "hg19") or path to fasta/indexed genome.
+  # @return [String] IGV response.
+  # @example
+  #   igv.genome("hg19")
+  #   igv.genome("/path/to/genome.fa")
   def genome(name_or_path)
     path = File.expand_path(name_or_path)
     if File.exist?(path)
@@ -189,12 +201,15 @@ class IGV
     end
   end
 
-  # Loads a data or session file by specifying a full path to a local file or a URL.
-  # @note IGV Batch command
+  # Load a data or session file by specifying a full path to a local file or a URL.
   #
-  # @param path_or_url [String] The path to a local file or a URL
-  # @param index [String] The index of the file
-
+  # @note IGV Batch command: load
+  # @param path_or_url [String] Path to a local file or a URL.
+  # @param index [String, nil] Optional index file path.
+  # @return [String] IGV response.
+  # @example
+  #   igv.load("http://example.com/data.bam")
+  #   igv.load("/path/to/data.bam", index: "/path/to/data.bai")
   def load(path_or_url, index: nil)
     path_or_url = if URI.parse(path_or_url).scheme
                     path_or_url
@@ -207,27 +222,38 @@ class IGV
     raise ArgumentError, "Invalid URI or file path: #{path_or_url}"
   end
 
-  # Go to the specified location
-  # @note IGV Batch command
+  # Go to the specified location or list of loci.
   #
-  # @param location [String] The location to go to.
-
-  def goto(*position)
-    send :goto, *position
+  # @note IGV Batch command: goto
+  # @param position [String] Locus or list of loci (e.g. "chr1:1000-2000").
+  # @return [String] IGV response.
+  # @example
+  #   igv.goto("chr1:1000-2000")
+  def goto(position)
+    send :goto, position
   end
   alias go goto
 
-  # Defines a region of interest bounded by the two loci
-  # @note IGV Batch command
+  # Define a region of interest bounded by the two loci.
   #
-  # @param chr [String] The chromosome of the region
-  # @param start [Integer] The start position of the region
-  # @param end_ [Integer] The end position of the region
-
+  # @note IGV Batch command: region
+  # @param chr [String] Chromosome name.
+  # @param start [Integer] Start position.
+  # @param end_ [Integer] End position.
+  # @return [String] IGV response.
+  # @example
+  #   igv.region("chr1", 100, 200)
   def region(chr, start, end_)
     send :region, chr, start, end_
   end
 
+  # Sort alignment or segmented copy number tracks.
+  #
+  # @note IGV Batch command: sort
+  # @param option [String] Sort option (e.g. "base", "position", "strand", "quality", "sample", "readGroup").
+  # @return [String] IGV response.
+  # @example
+  #   igv.sort("position")
   def sort(option = 'base')
     vop = %w[base position strand quality sample readGroup]
     raise "options is one of: #{vop.join(', ')}" unless vop.include? option
@@ -235,72 +261,97 @@ class IGV
     send :sort, option
   end
 
-  # Expands the given track.
-  # @note IGV Batch command
+  # Expand a given track. If not specified, expands all tracks.
   #
-  # @param track [String] The track to expand.
-  #                       If not specified, expands all tracks.
-
+  # @note IGV Batch command: expand
+  # @param track [String, nil] Track name (optional).
+  # @return [String] IGV response.
+  # @example
+  #   igv.expand
+  #   igv.expand("track1")
   def expand(track = nil)
     send :expand, track
   end
 
-  # Collapses a given track.
-  # @note IGV Batch command
+  # Collapse a given track. If not specified, collapses all tracks.
   #
-  # @param track [String] The track to collapse.
-  #                       If not specified, collapses all tracks.
-
+  # @note IGV Batch command: collapse
+  # @param track [String, nil] Track name (optional).
+  # @return [String] IGV response.
+  # @example
+  #   igv.collapse
+  #   igv.collapse("track1")
   def collapse(track = nil)
     send :collapse, track
   end
 
-  # Squish a given track.
-  # @note IGV Batch command
+  # Squish a given track. If not specified, squishes all annotation tracks.
   #
-  # @param track [String] The track to squish.
-  #                       If not specified, squishes all tracks.
-
+  # @note IGV Batch command: squish
+  # @param track [String, nil] Track name (optional).
+  # @return [String] IGV response.
+  # @example
+  #   igv.squish
+  #   igv.squish("track1")
   def squish(track = nil)
     send :squish, track
   end
 
   # Set the display mode for an alignment track to "View as pairs".
   #
-  # @param track [String] The track to set.
-  #                       If not specified, sets all tracks.
-
+  # @note IGV Batch command: viewaspairs
+  # @param track [String, nil] Track name (optional).
+  # @return [String] IGV response.
+  # @example
+  #   igv.viewaspairs
+  #   igv.viewaspairs("track1")
   def viewaspairs(track = nil)
     send :viewaspairs, track
   end
 
-  # @note IGV Batch command
-
+  # Create a new session. Unloads all tracks except the default genome annotations.
+  #
+  # @note IGV Batch command: new
+  # @return [self] Returns self for method chaining.
+  # @example
+  #   igv.new
   def new
     send :new
+    self
   end
 
-  # @note IGV Batch command
-
+  # Clear all loaded tracks and data.
+  #
+  # @note IGV Batch command: clear
+  # @return [self] Returns self for method chaining.
+  # @example
+  #   igv.clear
   def clear
     send :clear
+    self
   end
 
   # Exit (close) the IGV application and close the socket.
-  # @note IGV Batch command (modified)
-
+  #
+  # @note IGV Batch command: exit
+  # @return [nil] Exits IGV and closes the socket.
+  # @example
+  #   igv.exit
   def exit
     send :exit
     @socket.close
+    nil
   end
   alias quit exit
 
-  #	Sets the directory in which to write images.
-  # Returns the current snapshot directory if no argument is given.
-  # @note IGV Batch command (modified)
+  # Set or get the directory in which to write images (snapshots).
   #
-  # @param path [String] The path to the directory.
-
+  # @note IGV Batch command: snapshotDirectory
+  # @param dir_path [String, nil] Directory path. If nil, returns current snapshot directory.
+  # @return [String] IGV response or current directory.
+  # @example
+  #   igv.snapshot_dir("/tmp/snapshots")
+  #   igv.snapshot_dir #=> "/tmp/snapshots"
   def snapshot_dir(dir_path = nil)
     return @snapshot_dir if dir_path.nil?
 
@@ -314,136 +365,269 @@ class IGV
 
   private def snapshot_dir_internal(dir_path)
     dir_path = File.expand_path(dir_path)
+    warn "[ruby-igv] Directory #{dir_path} does not exist. Creating it." unless File.exist?(dir_path)
     FileUtils.mkdir_p(dir_path)
     send :snapshotDirectory, dir_path
   end
 
-  # Saves a snapshot of the IGV window to an image file.
-  # If filename is omitted, writes a PNG file with a filename generated based on the locus.
-  # If filename is specified, the filename extension determines the image file format,
-  # which must be either .png or .svg.
-  # @note IGV Batch command (modified)
-  # @note In Ruby-IGV, it is possible to pass absolute or relative paths as well as file names;
-  #       the Snapshot directory is set to Dir.pwd by default.
+  # Save a snapshot of the IGV window to an image file.
   #
-  # @param file_path [String] The path to the image file.
+  # @note IGV Batch command: snapshot
+  # @param file_name [String, nil] Name of the image file. If nil, uses the current locus.
+  #   If filename is omitted, writes a PNG file with a filename generated based on the locus.
+  #   If filename is specified, the filename extension determines the image file format, which must be either .png or .svg.
+  #   Passing a path might work, but is not recommended.
+  # @example
+  #   igv.snapshot("region.png")
+  def snapshot(file_name = nil)
+    return send(:snapshot) if file_name.nil?
+    dir_path = File.dirname(file_name)
+
+    # file_name is a file name
+    return send(:snapshot, file_name) if dir_path == "."
 
-  def snapshot(file_path = nil)
-    return send(:snapshot) if file_path.nil?
+    # file_name is a path
+    file_path = file_name
+    warn "[ruby-igv] snapshot: Passing a path is not recommended. "
+
+    if File.absolute_path?(file_path)
+      dir_path = File.expand_path(dir_path)
+    else
+      dir_path = File.expand_path(File.join(@snapshot_dir, dir_path))
+    end
 
-    dir_path = File.dirname(file_path)
     filename = File.basename(file_path)
-    if dir_path != @snapshot_dir
-      snapshot_dir_internal(dir_path)
-      r = send :snapshot, filename
-      snapshot_dir_internal(@snapshot_dir)
-      r
+    
+    # Only change directory if needed
+    if dir_path == @snapshot_dir
+      send(:snapshot, filename)
     else
-      send :snapshot, filename
+      # Temporarily change snapshot directory
+      original_dir = @snapshot_dir
+      snapshot_dir_internal(dir_path)
+      result = send(:snapshot, filename)
+      snapshot_dir_internal(original_dir)
+      result
     end
   end
 
   # Temporarily set the preference named key to the specified value.
-  # @note IGV Batch command
   #
-  # @param key [String] The preference name
-  # @param value [String] The preference value
-
+  # @note IGV Batch command: preference
+  # @param key [String] Preference key.
+  # @param value [String] Preference value.
+  # @return [String] IGV response.
+  # @see https://raw.githubusercontent.com/igvteam/igv/master/src/main/resources/org/broad/igv/prefs/preferences.tab
+  # @example
+  #   igv.preferences("SAM.READ_GROUP_COLOR", "sample")
   def preferences(key, value)
     send :preferences, key, value
   end
 
   # Show "preference.tab" in your browser.
-
   def show_preferences_table
     require 'launchy'
     Launchy.open('https://raw.githubusercontent.com/igvteam/igv/master/src/main/resources/org/broad/igv/prefs/preferences.tab')
   end
 
   # Save the current session.
-  # It is recommended that a full path be used for filename. IGV release 2.11.1
-  # @note IGV Batch command
   #
-  # @param filename [String] The path to the session file
-
+  # @note IGV Batch command: saveSession
+  # @param file_path [String] Path to the session file.
+  # @return [String] IGV response.
+  # @example
+  #   igv.save_session("session.xml")
   def save_session(file_path)
     file_path = File.expand_path(file_path)
     send :saveSession, file_path
   end
 
-  # @note IGV Batch command
-
+  # Set the track "altColor", used for negative values in a wig track or negative strand features.
+  #
+  # @note IGV Batch command: setAltColor
+  # @param color [String] Color string (e.g. "255,0,0" or "FF0000").
+  # @param track [String] Track name.
+  # @return [String] IGV response.
+  # @example
+  #   igv.set_alt_color("255,0,0", "track1")
   def set_alt_color(color, track)
     send :setAltColor, color, track
   end
 
-  # @note IGV Batch command
-
+  # Set the track color.
+  #
+  # @note IGV Batch command: setColor
+  # @param color [String] Color string (e.g. "255,0,0" or "FF0000").
+  # @param track [String] Track name.
+  # @return [String] IGV response.
+  # @example
+  #   igv.set_color("FF0000", "track1")
   def set_color(color, track)
     send :setColor, color, track
   end
 
-  # @note IGV Batch command
-
+  # Set the data range (scale) for all numeric tracks, or a specific track.
+  #
+  # @note IGV Batch command: setDataRange
+  # @param range [String] Range string (e.g. "0,100" or "auto").
+  # @param track [String] Track name.
+  # @return [String] IGV response.
+  # @example
+  #   igv.set_data_range("0,100", "track1")
   def set_data_range(range, track)
     send :setDataRange, range, track
   end
 
-  # @note IGV Batch command
-
+  # Set the data scale to log (true) or linear (false).
+  #
+  # @note IGV Batch command: setLogScale
+  # @param bool [Boolean] true for log scale, false for linear.
+  # @param track [String] Track name (optional).
+  # @return [String] IGV response.
+  # @example
+  #   igv.set_log_scale(true, "track1")
   def set_log_scale(bool, track)
     bool = 'true' if bool == true
     bool = 'false' if bool == false
     send :setLogScale, bool, track
   end
 
-  # @note IGV Batch command
-
+  # Set the sequence strand to positive (+) or negative (-).
+  #
+  # @note IGV Batch command: setSequenceStrand
+  # @param strand [String] "+" or "-".
+  # @return [String] IGV response.
+  # @example
+  #   igv.set_sequence_strand("+")
   def set_sequence_strand(strand)
     send :setSequenceStrand, strand
   end
 
-  # @note IGV Batch command
-
+  # Show or hide the 3-frame translation rows of the sequence track.
+  #
+  # @note IGV Batch command: setSequenceShowTranslation
+  # @param bool [Boolean] true to show, false to hide.
+  # @return [String] IGV response.
+  # @example
+  #   igv.set_sequence_show_translation(true)
   def set_sequence_show_translation(bool)
     bool = 'true' if bool == true
     bool = 'false' if bool == false
     send :setSequenceShowTranslation, bool
   end
 
-  # @note IGV Batch command
-
+  # Set a delay (sleep) time in milliseconds between successive commands.
+  #
+  # @note IGV Batch command: setSleepInterval
+  # @param ms [Integer] Milliseconds to sleep.
+  # @return [String] IGV response.
+  # @example
+  #   igv.set_sleep_interval(200)
   def set_sleep_interval(ms)
     send :setSleepInterval, ms
   end
 
-  # @note IGV Batch command
-
+  # Set the specified track's height in integer units.
+  #
+  # @note IGV Batch command: setTrackHeight
+  # @param height [Integer] Height in pixels.
+  # @param track [String] Track name.
+  # @return [String] IGV response.
+  # @example
+  #   igv.set_track_height(50, "track1")
   def set_track_height(height, track)
     send :setTrackHeight, height, track
   end
 
-  # @note IGV Batch command
-
+  # Set the number of vertical pixels (height) of each panel to include in image.
+  #
+  # @note IGV Batch command: maxPanelHeight
+  # @param height [Integer] Height in pixels.
+  # @return [String] IGV response.
+  # @example
+  #   igv.max_panel_height(2000)
   def max_panel_height(height)
     send :maxPanelHeight, height
   end
 
-  # @note IGV Batch command
-
+  # Set the "color by" option for alignment tracks.
+  #
+  # @note IGV Batch command: colorBy
+  # @param option [String] Color by option (e.g. "SAMPLE", "READ_GROUP", "TAG", ...).
+  # @param tag [String, nil] Tag name (required for option "TAG").
+  # @return [String] IGV response.
+  # @example
+  #   igv.color_by("SAMPLE")
+  #   igv.color_by("TAG", "NM")
   def color_by(option, tag)
     send :colorBy, option, tag
   end
 
-  # @note IGV Batch command
-
+  # Group alignments by the specified option.
+  #
+  # @note IGV Batch command: group
+  # @param option [String] Group option (e.g. "SAMPLE", "READ_GROUP", "TAG", ...).
+  # @param tag [String, nil] Tag name or position (required for option "TAG").
+  # @return [String] IGV response.
+  # @example
+  #   igv.group("SAMPLE")
+  #   igv.group("TAG", "NM")
   def group(option, tag)
     send :group, option, tag
   end
 
-  # @note IGV Batch command
-
+  # Overlay a list of tracks.
+  #
+  # @note IGV Batch command: overlay
+  # @param overlaid_track [String] The track to overlay.
+  # @param tracks [Array<String>] List of tracks to overlay.
+  # @return [String] IGV response.
+  # @example
+  #   igv.overlay("track1", "track2", "track3")
   def overlay(overlaid_track, *tracks)
     send :overlay, overlaid_track, *tracks
   end
+
+  # Scroll all panels to the top of the view.
+  #
+  # @note IGV Batch command: scrollToTop
+  # @return [String] IGV response.
+  # @example
+  #   igv.scroll_to_top
+  def scroll_to_top
+    send :scrollToTop
+  end
+
+  # Separate an overlaid track into its constituitive tracks.
+  #
+  # @note IGV Batch command: separate
+  # @param overlaid_track_name [String] The name of the overlaid track to separate.
+  # @return [String] IGV response.
+  # @example
+  #   igv.separate("track1")
+  def separate(overlaid_track_name)
+    send :separate, overlaid_track_name
+  end
+
+  # Set an access token to be used in an Authorization header for all requests to host.
+  #
+  # @note IGV Batch command: setAccessToken
+  # @param token [String] The access token.
+  # @param host [String, nil] The host to use the token for (optional).
+  # @return [String] IGV response.
+  # @example
+  #   igv.set_access_token("mytoken", "example.com")
+  def set_access_token(token, host = nil)
+    send :setAccessToken, token, host
+  end
+
+  # Clears all access tokens.
+  #
+  # @note IGV Batch command: clearAccessTokens
+  # @return [String] IGV response.
+  # @example
+  #   igv.clear_access_tokens
+  def clear_access_tokens
+    send :clearAccessTokens
+  end
 end

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: ruby-igv
 version: !ruby/object:Gem::Version
-  version: 0.0.9
+  version: 0.0.10
 platform: ruby
 authors:
 - kojix2
-autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-04-24 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: launchy
@@ -95,7 +94,6 @@ homepage: https://github.com/kojix2/ruby-igv
 licenses:
 - MIT
 metadata: {}
-post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -110,8 +108,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.5
-signing_key:
+rubygems_version: 3.6.7
 specification_version: 4
 summary: Control IGV (Integrative Genomics Viewer) with Ruby.
 test_files: []