bioinfologics/sdg

Issues

• redesign views

  #135 opened 4 years ago by bjclavijo
  0

• Add rle capability to long read datastores

  #134 opened 4 years ago by bjclavijo
  0

• Possible overflow in ws.ls()

  #128 opened 4 years ago by jonwright99
  1

• Kci to take kmer counter index as argument or somethign similar

  #133 opened 4 years ago by gonzalogacc
  0

• Installation issue

  #132 opened 4 years ago by chrisquince
  1

• segfault when making a workspace including a long read datastore

  #129 opened 4 years ago by jonwright99
  0

• Unify all kmer generation from strings/char* in a KmerIterator class template

  #126 opened 4 years ago by bjclavijo
  0

• GraphPatcher

  #125 opened 4 years ago by bjclavijo
  0

• sdg-dbg allows kmer size>63

  #124 opened 4 years ago by jonwright99
  0

• all datastores to return RC sequence when using negative read ids

  #123 opened 4 years ago by bjclavijo
  0

• check seqID_T is used everywhere to refer to read ids

  #122 opened 4 years ago by bjclavijo
  0

• Adaptor for sam mappings loading

  #76 opened 4 years ago by bjclavijo
  2

• support multiple files on datastore make

  #120 opened 5 years ago by bjclavijo
  0

• sdg-kmercounter status not working

  #118 opened 5 years ago by jonwright99
  0

• Segfault on OSX

  #109 opened 5 years ago by TransGirlCodes
  1

• Adding a datastore gives an .bsgws as output, not .sdgws

  #117 opened 5 years ago by jonwright99
  0

• Name inconsistency kmer counts api

  #114 opened 5 years ago by gonzalogacc
  0

• review and create a set of coherent CLI tools only

  #78 opened 5 years ago by bjclavijo
  0

• Create a v1.0 release and pre-compiled binaries + lib

  #103 opened 5 years ago by bjclavijo
  3

• Implement a NodeProxy class to use a node-centric approach to SDGs + DG

  #87 opened 5 years ago by bjclavijo
  2

• Add a list-contents and get_by_name functions to the ws

  #110 opened 5 years ago by gonzalogacc
  3

• Tidy read mapper's indexing and read mapping methods

  #104 opened 5 years ago by bjclavijo
  2

• selected_node parameter in write_to_gfa1 not accepting int vector

  #113 opened 5 years ago by gonzalogacc
  1

• Check that std::vector<std::string>> arguments to functions can be called with native vectors and native strings from python

  #112 opened 5 years ago by bjclavijo
  1

• datastore vector realloc corrupts datastores

  #107 opened 5 years ago by bjclavijo
  2

• GFA v1 and v2 I/O

  #73 opened 5 years ago by bjclavijo
  3

• Separate LinkageMaker and LinkageUntangler

  #99 opened 5 years ago by bjclavijo
  1

• Make builds docs even when turned off

  #108 opened 5 years ago by TransGirlCodes
  0

• Min read size parameter not working for long reads

  #111 opened 5 years ago by gonzalogacc
  0

• SDG.LinkedReadsDatastore_build_from_fastq never ends

  #106 opened 5 years ago by gonzalogacc
  2

• Linked reads DS data format

  #105 opened 5 years ago by gonzalogacc
  1

• Include circles when creating unitigs in the graph maker

  #101 opened 5 years ago by TransGirlCodes
  2

• LDGs do not extend their link vector past the last link

  #72 opened 5 years ago by bjclavijo
  0

• remove 7bp from r1 of 10x reads after the tag

  #74 opened 5 years ago by bjclavijo
  0

• Deprecate log for OperationJournals

  #100 opened 5 years ago by bjclavijo
  0

• Remove all unnecessary uses of 'this->', and rename arguments to functions that disambiguate with it.

  #96 opened 5 years ago by bjclavijo
  1

• Create an OperationJournal class to save support on the WS

  #95 opened 5 years ago by bjclavijo
  0

• Load paths from w2rap-contigger

  #77 opened 5 years ago by bjclavijo
  3

• Make the LongReadDatastore skip read 0 (for consistency)

  #91 opened 5 years ago by bjclavijo
  0

• LongReadsDatastore::get_read_sequence -> make it work like in all other datastores

  #93 opened 5 years ago by bjclavijo
  0

• Replace the individual Buffered getters in all code by ReadSequenceBuffer

  #92 opened 5 years ago by bjclavijo
  0

• Persist DGs in the workspace

  #67 opened 5 years ago by bjclavijo
  1

• Persist tag neighbours in workspace

  #71 opened 5 years ago by bjclavijo
  0

• add get_read_seq to EVERY datastore

  #81 opened 5 years ago by bjclavijo
  0

• make sure build_form_fastq can deal with .gz files

  #82 opened 5 years ago by bjclavijo
  0

• sdg-datastore to detect read length automatically

  #79 opened 5 years ago by bjclavijo
  0

• make all API functions receive output filenames first

  #80 opened 5 years ago by bjclavijo
  0

• Optimise long read mapping (speed)

  #75 opened 5 years ago by bjclavijo
  0

• review usage of std::set and std::unordered_set, and their mapping through SWIG

  #69 opened 5 years ago by bjclavijo
  2

• create GFA output of a MLGD -> Anchor -> LDG -> Backbone -> consensus process

  #68 opened 5 years ago by bjclavijo
  0