Update documentation for filterAlignments. This fixes #267 #277 (#282)

* Update documentation for filterAlignments. This fixes #267 #277
milaboratory · Nov 22, 2017 · 350cccf · 350cccf
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diff --git a/CHANGELOG_CURRENT b/CHANGELOG_CURRENT
@@ -1 +1,2 @@
-minor: Added proper filtering for alleles with wildcard symbols in `featureToAlign` region
+minor: Added proper filtering for alleles with wildcard symbols in `featureToAlign` region
+minor: Documentation added for `filterAlignments`
diff --git a/doc/index.rst b/doc/index.rst
@@ -18,11 +18,6 @@ MiXCR is free for academic and non-profit use (see :ref:`License <license>`).
 
    *MiXCR pipeline. The workflow from IG or T-cell receptor data sets to final clonotypes is shown*
 
-:ref:`getting-started`
-:ref:`main-actions`
-:ref:`special-cases`
-:ref:`in-depth-topics`
-
 .. _getting-started:
 
 .. toctree::

diff --git a/doc/utils.rst b/doc/utils.rst
@@ -47,3 +47,31 @@ Allows to merge multiple ``.vdjca`` files into a single one:
     > mixcr mergeAlignments file1.vdjca file2.vdjca ... output.vdjca
 
 
+Filter alignments
+-----------------
+
+Allows to filter alignments in ``.vdjca`` file. Example:
+
+::
+
+    > mixcr filterAlignments --chains TRA,TRB input_file.vdjca output_file.vdjca
+
+The available options are:
+
++--------------------------------+-------------------------------------------------------------------------------------------------+
+| Option                         | Description                                                                                     |
++================================+=================================================================================================+
+| ``-e``, ``--cdr3-equals``      | Include only those alignments which CDR3 equals to a specified nucleotide sequence              |
++--------------------------------+-------------------------------------------------------------------------------------------------+
+| ``c``, ``--chains``            | Include only alignments with specified immunological protein chains (comma separated list       |
+|                                | of some of IGH, IGL, IGK, TRA, TRB, TRG, TRD chains)                                            |
++--------------------------------+-------------------------------------------------------------------------------------------------+
+| ``-x``, ``--chimeras-only``    | Output only chimeric alignments                                                                 |
++--------------------------------+-------------------------------------------------------------------------------------------------+
+| ``-g``, ``--contains-feature`` | Include only those alignments that contain specified gene feature (see :ref:`ref-geneFeatures`) |
++--------------------------------+-------------------------------------------------------------------------------------------------+
+| ``-i``, ``--read-ids``         | Output alignments with specified IDs only                                                       |
++--------------------------------+-------------------------------------------------------------------------------------------------+
+| ``-n``, ``--limit``            | Maximal number of alignments to process                                                         |
++--------------------------------+-------------------------------------------------------------------------------------------------+
+