Merge branch 'feature/#8' into develop

CHANGELOG_CURRENT

@@ -0,0 +1,6 @@
+New feature (#8 and #36) that allows to extract actual reads that were used in each clone (for more details see updated documentation)
+Added new action `exportReads` which export initial reads aggregated by each clones to separate .fastq files
+Added new export options for `exportAlignments`: `-cloneId` (prints clone ID that aggregated corresponding alignment) and `-mapping` (same, with additional info on mapping type)
+Added new export option for `exportClones`: `-mapping` will pring all alignment IDs that were aggreafated by clone
+Added option `-n` (print only first n rows) to all `export` commands
+minor: minor improvements and bug fixes

doc/align.rst

@@ -65,6 +65,10 @@ The following table contains description of command line options for ``align``:
 |                                  |                            | ``-descrR1`` and ``-descrR2`` options in                   |
 |                                  |                            | :ref:`exportAlignments <ref-export>` action).              |
 +----------------------------------+----------------------------+------------------------------------------------------------+
+| ``-g``, ``--save-reads``         |                            | Copy read(s) from ``.fastq`` or ``.fasta`` to ``.vdjca``   |
+|                                  |                            | file (this is required for exporting reads aggregated by   |
+|                                  |                            | clones; see :ref:`this section <ref-exporting-reads>`).    |
++----------------------------------+----------------------------+------------------------------------------------------------+
 | ``-Oparameter=value``            |                            | Overrides default value of aligner ``parameter``           |
 |                                  |                            | (see next subsection).                                     |
 +----------------------------------+----------------------------+------------------------------------------------------------+
@@ -194,8 +198,8 @@ parameters. It contains the following parameters:
 |                  |                                        |    other elements equal to ``mismatch``                                     |
 |                  |                                        |  - ``raw`` --- a complete set of 16 matrix elements should be specified;    | 
 |                  |                                        |    for  example:                                                            |
-|                  |                                        |   ``raw(5,-9,-9,-9,-9,5,-9,-9,-9,-9,5,-9,-9,-9,-9,5)``                      |
-|                  |                                        |   (*equivalent to the  default value*)                                      |
+|                  |                                        |    ``raw(5,-9,-9,-9,-9,5,-9,-9,-9,-9,5,-9,-9,-9,-9,5)``                     |
+|                  |                                        |    (*equivalent to the  default value*)                                     |
 +------------------+----------------------------------------+-----------------------------------------------------------------------------+
 | ``gapPenalty``   | ``-12``                                | Penalty for gap.                                                            |
 +------------------+----------------------------------------+-----------------------------------------------------------------------------+

doc/assemble.rst

@@ -88,6 +88,9 @@ The command line options of ``assemble`` are the following:
 +-------------------------+-------------------------------+--------------------------------------------------------------------------------+
 | ``-t``, ``--threads``   | number of available CPU cores | Number of processing threads.                                                  |
 +-------------------------+-------------------------------+--------------------------------------------------------------------------------+
+| ``-i``, ``--index``     |                               | Specify file which will store information about particular reads aggreagated   |
+|                         |                               | by each clone (mapping readId -> cloneId).                                     |
++-------------------------+-------------------------------+--------------------------------------------------------------------------------+
 | ``-Oparameter=value``   |                               | Overrides default value of assembler ``parameter`` (see next subsection).      |
 +-------------------------+-------------------------------+--------------------------------------------------------------------------------+