stuff.todo

BubbleGun TODO list:

 ✔ Fix chain coverages as it's over a 100% because of children and parents
 ✔ Fix gam digest, it should take the JSON file now and use the information there
 ✔ Output information such as the arguments given and the input output files in the log

 ☐ finding children should be done several times, or maybe the code revised
 ☐ Add and average the coverage when compacting
 ✔ Fix output haplotypes and fasta bubbles output:
 ☐ Solve superbubbles according to coverage (try using the mean k-mer coverage)
 ✔ Setup script
 ✔ Proper docstring comments on the code, use reST recommended by pep287
  """
  This is a reST style.

  :param param1: this is a first param
  :param param2: this is a second param
  :returns: this is a description of what is returned
  :raises keyError: raises an exception
  """
  #code

 ✔ Split modules into a directory @done (19-12-19 20:36)
 ✔ Turn options in main to argparser instead of optparser @done (20-01-15 16:18)
   ✔ GFA or VG file @done (19-12-19 21:19)
   ✔ K value (if not given then consider 0) @done (19-12-19 21:19)
   ✔ BFS neighbor extraction @done (19-12-20 16:01)

 ✔ Add functionality to Graph class @done (19-12-24 19:17)
   ✔ Add find bubble to graph (now graph.find_chains()) @done (19-12-19 23:13)
   ✔ Add compact graph to graph @done (19-12-20 16:02)
   ✔ Add remove lonely nodes @done (19-12-20 00:00)
   ✔ Output graph @done (19-12-24 19:17)

 ✔ Sort Bubble chain function @done (20-01-10 16:20)
 ✔ Path extractor function (takes a path, returns sequence) @done (20-02-06 16:59)
 ✔ Separate classes into separate modules in core @done (19-12-19 22:53)
 ✔ Fill in examples at after the print example command @done (20-01-22 14:24)
 ✔ Option for only detecting bubbles @done (20-01-22 14:24)

 ✔ Implement the low-memory bubbles detection version (compare both versions).
 ✔ Output bubbles as JSON.
 ✔ Implement the nested bubbles detection (hash chains with their ends).
 ✔ See what information can be removed from the node object
 ✔ Let user output certain chains based on id
 ✔ Option to only detect Superbubbles.
 ✔ Implement the low memory version.

 ✔ Add BFS search in graph @done (19-12-24 19:17)
 ✔ Add components and biggest component functionality @done (19-12-24 19:15)
 ✔ Read VG files  @done (20-01-10 16:20)
 ✔ Make sure not to write edges to removes nodes @done (19-12-19 23:52)
   ✔ function 'remove_node(node_id)' to graph that removes nodes and their edges @done (19-12-19 23:52)
 ✔ Start main.py @done (20-01-10 16:21)
 ✔ I need to compact the graph first before finding bubbles. @done (20-01-10 16:21)
 ✔ Maybe re-write the compactness script. Now it's a while loop instead of a nested function @done (20-01-22 14:24)
 ✔ Have a k check, if one of the nodes is smaller than k return an error and stop (can be done while reading the nodes) @done (20-01-15 16:18)

 ✔ Alignment file stuff: (20-02-12 11:34)
   ✔ Filter alignment less than 200 bp @done (20-02-12 11:34)
   ✔ Keep only the longest alignment if two alignments were mapped to the same chain (20-02-12 11:34)

Bugs:
 ✔ compacting didn't work on the graph, need to debug @done (19-12-20 17:15) 
 ✔ I can't read VG files for some reason, getting google.protobuff error @done (20-01-10 16:20)