Igdiscover

-----------------

* Implemented allele ratio filtering for J gene discovery
* J genes are discovered as part of the pipeline (previously, one needed
to run the ``discoverj`` script manually)
* In each iteration, dendrograms are now created not only for V genes, but
also for D and J genes. The file names are ``dendrogram_D.pdf``,
``dendrogram_J.pdf``
* The V dendrograms are now in ``dendrogram_V.pdf`` (no longer
``V_dendrogram.pdf``). This puts all the dendrograms together when looking
at the files in the iteration directory.
* The ``V_usage.tab`` and ``V_usage.pdf`` files are no longer created.
Instead, ``expressed_V.tab`` and ``expressed_V.pdf`` are created. These
contain similar information, but an allele-ratio filter is used to
filter out artifacts.
* Similarly, ``expressed_D.tab`` and ``expressed_J.tab`` and their
``.pdf`` counterparts are created in each iteration.
* Removed ``parse`` subcommand (functionality is in the ``igblast`` subcommand)
* New CDR3 detection method (only heavy chain sequences): CDR3 start/end coordinates
are pre-computed using the database V and J sequences. Increases detection rate
to 99% (previously less than 90%).
* Remove the ability to check discovered genes for required motifs. This has never
worked well.
* Add a column ``clonotypes`` to the ``candidates.tab`` that tries to count how many
clonotypes are associated with a single candidate (using only exact occurrences).
This is intended to replace the ``CDR3s_exact`` column.
* Add an ``exact_ratio`` to the germline filtering options. This checks the ratio
between the exact V occurrence counts (``exact`` column) between alleles.
* Germline filtering option ``allele_ratio`` was renamed to ``clonotypes_ratio``
* Implement a cache for IgBLAST results. When the same dataset is re-analyzed,
possibly with different parameters, the cached results are used instead of
re-running IgBLAST, which saves a lot of time. If the V/D/J database or the
IgBLAST version has changed, results are not re-used.

-------------------

* Add a ``barcodes_exact`` column to the candidates table. It gives the number
of unique barcode sequences that were used by the sequences in the set of
exact sequences. Also, add a configuration setting ``barcode_consensus``
that can turn off consensus taking of barcode groups, which needs to be
set to ``false`` for ``barcodes_exact`` to work.
* Add a ``Ds_exact`` column to candidates table.
* Add a ``D_coverage`` configuration option.
* The pre-processing filtering step no longer reads in the full table of
IgBLAST assignments, but filters the table piece by piece. Memory usage
for this step therefore does not depend anymore on the dataset size and
should always be below 1 GB.
* The functionality of the ``parse`` subcommand has been integrated into
the ``igblast`` subcommand. This means that ``igdiscover igblast`` now
directly outputs a result table (``assigned.tab``). This makes it easier
to use that subcommand directly instead of only via the workflow.
* The ``igblast`` subcommand now always runs ``makeblastdb`` by itself
and deletes the BLAST database afterwards. This reduces clutter and
ensures the database is always up to date.
* Remove the ``library_name`` configuration setting. Instead, the
``library_name`` is now always the same as the name of analysis
directory.

-------------------

* Add an “allele ratio” criterion to the germline filter to further reduce
the number of false positives. The filter is activated by default and can
be configured through the ``allele_ratio`` setting in the configuration
file. :ref:`See the documentation for how it works <allele-ratio>`.
* Ignore the CDR3-encoding bases whenever comparing two V gene sequences.
* Avoid finding 5'-truncated V genes by extending found hits towards the
5' end.
* By default, candidate sequences are no longer merged if they are nearly
identical. That is, the ``differences`` setting within the two germline
filter configuration sections is now set to zero by default.
Previously, we believed the merging would remove some false
positives, but it turns out we also miss true positives. It also seems
that with the other changes in this version we also no longer get the
particular false positives the setting was supposed to catch.
* Implement an experimental ``discoverj`` script for J gene discovery.
It is curently not run automatically as part of ``igdiscover run``. See
``igdiscover discoverj --help`` for how to run it manually.
* Add a ``config`` subcommand, which can be used to change the
configuration file from the command-line.
* Add a ``V_CDR3_start`` column to the ``assigned.tab``/``filtered.tab``
tables. It describes where the CDR3 starts within the V sequence.
* Similarly, add a ``CDR3_start`` column to the ``new_V_germline.tab``
file describing where the CDR3 starts within a discovered V sequence.
It is computed by using the most common CDR3 start of the
sequences within the cluster.
* Rename the ``compose`` subcommand to ``germlinefilter``.
* The ``init`` subcommand automatically fixes certain problems in the
input database (duplicate sequences, empty records, duplicate sequence
names). Previously, it would complain, but the user would have to fix
the problems themselves.
* Move source code to GitHub
* Set up automatic code testing (continuous integration) via Travis
* Many documentation improvements

-------------------

* The FASTA files of the input V/D/J gene lists now need to be
named ``V.fasta``, ``D.fasta`` and ``J.fasta``. The species name
is no longer part of the file name. This should reduce confusion
when working with species not supported by IgBLAST.
* The ``species:`` configuration setting in the configuration can
(and should) now be left empty. Its only use was that it is passed
to IgBLAST, but since IgDiscover provides IgBLAST with its own
V/D/J sequences anyway, it does not seem to make a difference.
* A “cross-mapping” detection has been added, which should reduce
the number of false positives.
:ref:`See the documentation for an explanation <cross-mapping>`.
* Novel sequences identical to a database sequence no longer get the
``_S1234`` suffix.
* No longer trim trim the initial ``G`` run in sequences (due to RACE) by
default. It is now a configuration setting.
* Add ``cdr3_location`` configuration setting: It allows to set whether to
use a CDR3 in addition to the barcode for grouping sequences.
* Create a ``groups.tab.gz`` file by default (describing the de-barcoded
groups)
* The pre-processing filter is now configurable. See the
``preprocessing_filter`` section in the configuration file.
* Many improvements to the documentation
* Extended and fixed unit tests. These are now run via a CI system.
* Statistics in JSON format are written to ``stats/stats.json``.
* IgBLAST 1.5.0 output can now be parsed. Parsing is also faster by 25%.
* More helpful warning message when no sequences were discovered in
an iteration.
* Drop support for Python 3.3.

-----------------

* V sequences of the input database are now whitelisted by default.
The meaning of the ``whitelist`` configuration option has changed:
If set to ``false``, those sequences are no longer whitelisted.
To whitelist additional sequences, create a ``whitelist.fasta``
file as before.
* Sequences with stop codons are now filtered out by default.
* Use more stringent germline filtering parameters by default.

-----------------

* It is now possible to install and run IgDiscover on OS X. Appropriate Conda
packages are available on bioconda.
* Add column ``has_stop`` to ``candidates.tab``, which indicates whether the
candidate sequence contains a stop codon.
* Add a configuration option that makes it possible to disable the 5' motif
check by setting ``check_motifs: false`` (the ``looks_like_V`` column is
ignored in this case).
* Make it possible to whitelist known sequences: If a found gene candidate
appears in that list, the sequence is included in the list of discovered
sequences even when it would otherwise not pass filtering criteria. To enable
this, just add a ``whitelist.fasta`` file to the project directory before
starting the analysis.
* The criteria for germline filter and pre-germline filter are now configurable:
See ``germline_filter`` and ``pre_germline_filter`` sections in the
configuration file.
* Different runs of IgDiscover with the same parameters on the same input files
will now give the same results. See the ``seed`` parameter in the configuration,
also on how to get non-reproducible results as before.
* Both the germline and pre-germline filter are now applied in each iteration.
Instead of the ``new_V_database.fasta`` file, two files named
``new_V_germline.fasta`` and ``new_V_pregermline.fasta`` are created.
* The ``compose`` subcommand now outputs a filtered version of the
``candidates.tab`` file in addition to a FASTA file. The table
contains columns **closest_whitelist**, which is the name of the closest
whitelist sequence, and **whitelist_diff**, which is the number of differences
to that whitelist sequence.