diff --git a/docs/guide.rst b/docs/guide.rst index d2087b8..eddee65 100644 --- a/docs/guide.rst +++ b/docs/guide.rst @@ -6,7 +6,8 @@ User Guide The following subcommands are available in gaftools -* :ref:`index ` - indexing a GAF file for the view command. +* :ref:`find_path ` - Extracting base sequencing from node path. +* :ref:`index ` - Indexing a GAF file for the view command. * :ref:`order_gfa ` - Ordering GFA file using BO and NO tags. * :ref:`phase ` - Adding phase information of the reads from a haplotag TSV. * :ref:`realign ` - Realigning GAF alignments using wavefront alignment. @@ -28,6 +29,38 @@ Links to related resources: * `GFA v1.0 documentation `_ * `GFA v2.0 documentation `_ +Some of the tags used in GAF files are derieved from :code:`minimap2` defined `here `_ + + +.. _gaftools-find-path: + +gaftools find_path +================== + +This subcommand retrieves the base seqeunce of paths in the given GFA. + +Usage +----- + +The :code:`find_path` subcommand takes 2 obligatory inputs, a GFA file and node path (like :code:`">s82312s82312