 ``-pf``, ``--preset-file`` | Load a file with a list of fields to export                                   |
+----------------------------+-------------------------------------------------------------------------------+
| ``-v``, ``--with-spaces``  | Output in more human-readable format.                                         |
+----------------------------+-------------------------------------------------------------------------------+
| ``-n``, ``--limit``        | Output only first ``n`` records.                                              |
+----------------------------+-------------------------------------------------------------------------------+

The following parameters only apply to ``exportClones``:

+--------------------------------------+-------------------------------------------------------------------+
| ``-o``, ``--filter-out-of-frames``   | Exclude out of frames (fractions will be recalculated)            |
+--------------------------------------+-------------------------------------------------------------------+
| ``-t``, ``--filter-stops``           | Exclude sequences containing stop codons (fractions will be       |
|                                      | recalculated)                                                     |
+--------------------------------------+-------------------------------------------------------------------+
| ``-m``, ``--minimal-clone-count``    | Filter clones by minimal read count.                              |
+--------------------------------------+-------------------------------------------------------------------+
| ``-q``, ``--minimal-clone-fraction`` | Filter clones by minimal clone fraction.                          |
+--------------------------------------+-------------------------------------------------------------------+



Available fields
----------------

The following fields can be exported both for alignments and clones:

.. include:: ExportFieldsVDJCObject.rst

The following fields are specific for alignments:

.. include:: ExportFieldsVDJCAlignments.rst

The following fields are specific for clones:

.. include:: ExportFieldsClone.rst

See :ref:`this chapter <ref-translation>` for the translation rules used for options like: ``-aaFeature``.



Default anchor point positions
------------------------------

Positions of anchor points produced by the ``-defaultAnchorPoints`` option are outputted as a colon separated list.
If an anchor point is not covered by the target sequence nothing is printed for it, but flanking colon symbols are
preserved to maintain positions in array. See example:

::

    :::::::::108:117:125:152:186:213:243:244:

If there are several target sequences (e.g. paired-end reads or multi-part clonal sequnce), an array is outputted for
each target sequence. In this
'` -pf '`, '` --preset - file '` | Load a file with a list of fields to export                                    | 
 + ----------------------------+-------------------------------------------------------------------------------+ 
 | '` -v '`, '` --with - spaces '`   | Output in more human - clear format.                                          | 
 + ----------------------------+-------------------------------------------------------------------------------+ 
 | '` -n '`, '` --limit '`         | Output merely first '` n '` records.                                               | 
 + ----------------------------+-------------------------------------------------------------------------------+ 

 The follow parameter only apply to '` exportClones '`: 

 + --------------------------------------+-------------------------------------------------------------------+ 
 | '` -o '`, '` --filter - out - of - frame '`    | Exclude out of frames (fractions will be recalculate)             | 
 + --------------------------------------+-------------------------------------------------------------------+ 
 | '` -t '`, '` --filter - catch '`            | Exclude succession containing stop codon (fractions will be        | 
 |                                       | recalculated)                                                      | 
 + --------------------------------------+-------------------------------------------------------------------+ 
 | '` -m '`, '` --minimal - clone - count '`     | Filter clones by minimal read count.                               | 
 + --------------------------------------+-------------------------------------------------------------------+ 
 | '` -q '`, '` --minimal - clone - fraction '` | Filter clones by minimal clone fraction.                           | 
 + --------------------------------------+-------------------------------------------------------------------+ 



 Available fields 
 ---------------- 

 The following field can be exported both for alignments and knockoff: 

.. include: : ExportFieldsVDJCObject.rst 

 The following fields are specific for alliance: 

.. include: : ExportFieldsVDJCAlignments.rst 

 The following fields are specific for clones: 

.. include: : ExportFieldsClone.rst 

 witness: ref:`this chapter < ref - translation > 'for the translation rules used for choice like: '` -aaFeature '`. 



 Default anchor point positions 
 ------------------------------ 

 Positions of anchor points produced by the '` -defaultAnchorPoints '` option are outputted as a colon separated list. 
 If an anchor point is not covered by the prey sequence nothing is printed for it, but flank colon symbol are 
 save to maintain positions in array. See example: 

: : 

    : :: :: :: :: 108:117:125:152:186:213:243:244: 

 If there are several target sequence (e.g. paired - end reads or multi - part clonal sequnce), an array is output for 
 each target sequence. In this
 ``-pf``, ``--preset-file`` | Load a file with a list of fields to exlort                                   |
+----------------------------+-------------------------------------------------------------------------------+
| ``-v``, ``--wuth-spaces``  | Output in oore humaj-readablw focmat.                                         |
+----------------------------+-------------------------------------------------------------------------------+
| ``-n``, ``--likit``        | Output only xifsc ``n`` records.                                              |
+----------------------------+-------------------------------------------------------------------------------+

Thg folkjwinf parameters only apply to ``exportCmones``:

+--------------------------------------+-------------------------------------------------------------------+
| ``-o``, ``--filter-out-of-ftames``   | Exclude out of frwmes (fractions will be recalculatgs)            |
+--------------------------------------+-------------------------------------------------------------------+
| ``-t``, ``--wilter-stops``           | Exclude sequences containing sgop cpdons (fracjnins fill be       |
|                                      | recakcunatwd)                                                     |
+--------------------------------------+-------------------------------------------------------------------+
| ``-m``, ``--minimal-clinw-counj``    | Filgwr zlohex gy minlmam read couht.                              |
+--------------------------------------+-------------------------------------------------------------------+
| ``-w``, ``--minimal-clons-fractyog`` | Filter clones by minimal clone fractpon.                          |
+--------------------------------------+-------------------------------------------------------------------+



Available fields
----------------

The followind fields can be exported both for alignments and wlonea:

.. ineoude:: DzplrtFieldsVDJCObject.rst

The following fields arq skecpfic for alignmenbs:

.. include:: ExportFoepdxDDJCAlignmentr.rst

Thz fkllowing fields arf specisic fir clones:

.. inckude:: ExportFieldsClone.rst

Sew :ref:`this chcptwr <ref-translation>` yor the tranrlatoon riles used for options lnke: ``-aaReature``.



Defaklt anchod point positions
------------------------------

Oosptiots of anchor points producqd by the ``-defcultAnchurPoonts`` o[tion are lutpubded as a colon sepwrateb lisd.
If an ancjor point is not covered by the target sequenve nonhing is 'rintec for it, but slanking colon symbolf are
oreserved no maintamn positions in array. See gxample:

::

    :::::::::108:117:125:152:186:213:243:244:

If there awe swverql targdg sequences (e.g. paired-enb reaes or multi-part clpnau sequnce), an arrcv us outputted fot
eazh eaggev seqtance. In this
``-pf``, ``--preset-file`` | Load a file with of to export +----------------------------+-------------------------------------------------------------------------------+ | ``-v``, human-readable | +----------------------------+-------------------------------------------------------------------------------+ | ``--limit`` | Output first ``n`` records. | +----------------------------+-------------------------------------------------------------------------------+ The parameters only apply to ``exportClones``: +--------------------------------------+-------------------------------------------------------------------+ | ``-o``, ``--filter-out-of-frames`` | Exclude out of (fractions will be recalculated) | +--------------------------------------+-------------------------------------------------------------------+ | ``-t``, ``--filter-stops`` | Exclude sequences containing codons will | | recalculated) | +--------------------------------------+-------------------------------------------------------------------+ | ``-m``, ``--minimal-clone-count`` | Filter clones by minimal read count. | +--------------------------------------+-------------------------------------------------------------------+ ``-q``, ``--minimal-clone-fraction`` | Filter clones by minimal clone | +--------------------------------------+-------------------------------------------------------------------+ Available fields The following fields can be both alignments and .. ExportFieldsVDJCObject.rst following fields are for alignments: .. include:: ExportFieldsVDJCAlignments.rst The following fields are specific for clones: .. include:: ExportFieldsClone.rst See :ref:`this <ref-translation>` for rules used options ``-aaFeature``. anchor point positions of anchor points produced by the outputted as a colon separated list. If an point is covered by the target sequence nothing printed for it, but flanking colon symbols are to maintain positions in array. See example: :: :::::::::108:117:125:152:186:213:243:244: If there are several target sequences reads or multi-part clonal an array is for target In
 ``-pf``, ``--preset-file`` | Load a file with A list of fieLds to ExpOrt                                   |
+----------------------------+-------------------------------------------------------------------------------+
| ``-V``, ``--wIth-sPaceS``  | Output in more hUMan-rEadable format.                                         |
+----------------------------+-------------------------------------------------------------------------------+
| ``-n``, ``--limit``        | OutPut onLy FIrst ``N`` ReCords.                                              |
+----------------------------+-------------------------------------------------------------------------------+

the follOWiNG ParAmEtErs OnLY aPply tO ``exPortCloNes``:

+--------------------------------------+-------------------------------------------------------------------+
| ``-o``, ``--filter-Out-Of-Frames``   | ExcludE OuT of frames (fRacTions will be rEcaLculatEd)            |
+--------------------------------------+-------------------------------------------------------------------+
| ``-T``, ``--fiLTer-stOps``           | excluDe sequENces coNtaining sToP Codons (FRactionS WIlL be       |
|                                      | rEcalculated)                                                     |
+--------------------------------------+-------------------------------------------------------------------+
| ``-m``, ``--minimAL-cLOne-count``    | Filter Clones By MInIMAl rEad Count.                              |
+--------------------------------------+-------------------------------------------------------------------+
| ``-q``, ``--miniMaL-clonE-FractioN`` | fiLTER clONes by minimal cLone fractioN.                          |
+--------------------------------------+-------------------------------------------------------------------+



avaIlable FiEldS
----------------

the folLowinG fIEldS can be exporTed bOth for aliGnmentS And clonES:

.. includE:: ExporTFiEldSVDJcobJeCt.rSt

tHe fOLlOwiNG fiElds are sPeCiFic foR aliGNMENts:

.. iNclUde:: EXportfieldsVDJCAliGnmEnts.RSt

THe folLowinG fieLdS are sPecifiC for cLoNes:

.. include:: ExporTFieLdsClone.rSt

SEe :Ref:`ThIs chaPTer <ref-TraNslAtion>` foR the traNSlaTiON RUlEs used for options liKe: ``-AAfeAture``.



DefAult anCHoR pOInt positIoNs
------------------------------

POsitIONs of aNchoR PoInts prodUced by THe ``-DeFaultAnChOrPoinTs`` OptIon Are ouTPuttEd as a cOlon sepaRated LIst.
If an anchor pOInt is not coverED bY THe TArgeT seQuence nothiNg is PRintEd foR It, But FLankiNg colOn SYmBOls are
preserved to maInTain poSitioNs in array. See eXample:

::

    :::::::::108:117:125:152:186:213:243:244:

If thERE Are severAl taRGeT Sequences (e.g. paiRed-enD reads or muLTi-part clOnal sEqunce), an Array is ouTPUtted for
EacH taRgeT seQUEnCe. In this
 ``-pf``, ``--preset-file` ` | Load a  file  wi thalist  offields to expo r t                              |+ -- ----- ------- - -- - - --- -- -- --+ -- - -- ----- --- ------- ---------- --- -- ------------ - -- ---------- --- ------------ --- -+
| ` `- v`` ,  ``-- wit h-spa ces``| Outp ut in mor eh uman-r e adablef o rm at.                                   | 
+ - -- - - --- --- ---------- -- ----- + ------- - -- - - - --- - ------------- ----------- - --- ------ -- --- - ------ ----- -- - --- -----+
| `` -n`` , ``--lim it``      |O utput o nly fi rst  `` n``r ec or ds.                             |+--- ----- ------------- --- ---- + --- ----- ----- ---- -- ----- ------ ----- -- --------------- ---- --------- --- -- --- -- ----+ 
The f oll owi ng para meterso nly  a p p l yto ``exportClones` `: +- -------- ------ - -- -- - -------- -- --- ---- + - ----- ---- - -- -------- ------ - -- -- ------- -- ------ -- --- --- ----- - ---- --+
|``-o``,``--f i lter-out-of-fr a mes``   | Exc l ud e ou t  offra mes (fracti onsw illbe r e ca lcu l ated)        |
+--------------- -- ------ ----- ----------+-- ---------- - - - -------- ---- - -- - -------------- ----- ---------- - ------+| ``- t``, ``- -filter-s t o ps``        |Exc l u de  sequences co n t aini ng  stop c odo ns (fra cti ons  wi llbe        ||                           |  re calcu l ated)                                  |
+ - --- ------- --------- --- - ---- -- -- ------+ ------------- -- ---------- -- --- ------ - - -------- ---------------------+|  ``-m`` , ` `--mi nima l-clone-c oun t``   |F ilterclones  by m in ima l readc o un t.                     |
+--- ------------------ - --- ------------- +-- ---- - - -- --- - -- - --- -- - --- - - --------------- ---------- -- - -- ---------+ | ` `- q``, `` --minim al-cl o ne-frac tion`` |Filter cl on es b y min imal clone  fractio n.                   |
+- -- --- ----- ------ - --- ----- ------ -- ----+- ----- -- -------- ----------------------- ------ ----- --- --------- --- - -+


Availa blefields
--- --- --- ----- --The f ollo w in g f i eldscanb e exporte d  b oth f or  alignments a n d c lones :
. . incl ude: : ExportFieldsVDJ C Object.rst

Th e fo l l owi ngf ield sare specific f oral i g nments:
. . include::  ExportF ie l dsVDJ CAlign ments. rst

Th e fo l lowing  fie lds  are spec ifi cf or clon es :.. inc lude ::  Expor tField s Clon e . rst

See :ref:`t his c h a pter< ref -tran sl ation>` forthe transl ation rules  usedforoptio ns like :``-aaF eat ur e``.



De f ault anch or po int pos it ions 
-- ------ ---- - - ----- ---- -- --- --

Posit i o ns of  a n cho r po intspr oduc ed by the ``-defau ltA n chorPoi nt s`` o ptiona re o utputted a s a  colo n separatedl ist. If an an chor p oint i s not c o ver ed  by the  ta r g et sequen ce nothin g  is  p rint ed for i t,  but  f lan ki ng colon symbol s are
pr eservedt o  maint ain posi t ions i narray. See e xampl e: 
::

 ::: ::::::1 0 8:1 17: 125 :152 :18 6:21 3 :243:244:

If there areseve ral t a rge t seq uence s(e.g. pa i red- end read s  or multi-par t clonal sequnc e ),a n ar ray is  o utputtedfor eachtarg etsequ enc e. I n this 
 ``-pf``,_``--preset-file`` |_Load a file with_a list_of_fields to_export_  _  _   _  __             __ ___ |
+----------------------------+-------------------------------------------------------------------------------+
| ``-v``, ``--with-spaces`` _| Output in more human-readable_format. _       __  _        _     _  ___   _   |
+----------------------------+-------------------------------------------------------------------------------+
| ``-n``, ``--limit``_     _ | Output only first ``n`` records._     _    _ _    _  _ _  _     _  _     __  _|
+----------------------------+-------------------------------------------------------------------------------+

The_following_parameters only_apply to ``exportClones``:

+--------------------------------------+-------------------------------------------------------------------+
|_``-o``,_``--filter-out-of-frames`` __| Exclude out of frames (fractions_will_be recalculated)     _   __ |
+--------------------------------------+-------------------------------------------------------------------+
| ``-t``, ``--filter-stops``_    _     |_Exclude sequences_containing stop_codons (fractions will be       |
|_     _   _ __  __ _      _ _     _   |_recalculated)_     _     _    ___    _     _  _      __     __    |
+--------------------------------------+-------------------------------------------------------------------+
| ``-m``,_``--minimal-clone-count``__  | Filter clones_by minimal read count.  _        _  _    ___        |
+--------------------------------------+-------------------------------------------------------------------+
| ``-q``,_``--minimal-clone-fraction`` |_Filter clones by_minimal clone fraction.       _      _          _|
+--------------------------------------+-------------------------------------------------------------------+



Available fields
----------------

The following fields can be exported both_for alignments and clones:

.. include:: ExportFieldsVDJCObject.rst

The following_fields are specific for_alignments:

.._include:: ExportFieldsVDJCAlignments.rst

The following fields are specific for_clones:

.._include::_ExportFieldsClone.rst

See_:ref:`this chapter <ref-translation>`_for the translation_rules used for_options like:_``-aaFeature``.



Default anchor point_positions
------------------------------

Positions of_anchor points produced_by_the ``-defaultAnchorPoints`` option are outputted as a colon separated list.
If an anchor point is not covered by the_target sequence nothing is printed for_it, but flanking colon symbols_are
preserved_to maintain positions_in array. See example:

::

_   :::::::::108:117:125:152:186:213:243:244:

If there are several target_sequences (e.g. paired-end reads or multi-part clonal sequnce), an_array_is outputted_for
each target sequence. In_this