Commit 0f6fc808 authored by Mikaël Salson's avatar Mikaël Salson

dev.org: Some (sparse) developer documentation

parent 2c9bf5b8
* Algorithm
** Code organisation
The algorithm follows roughly those steps:
1. The germlines are read. germlines are in the fasta format and are read
by the Fasta class (=core/fasta.h=). Germlines are built using the
Germline (or MultiGermline) class (=core/germline.h=)
2. The input sequence file (.fasta, .fastq, .gz) is read by an OnlineFasta
(=core/fasta.h=). The difference with the Fasta class being that all the
data is not stored in memory but the file is read online, storing only
the current entry.
3. Windows must be extracted from the read, which is done by the
WindowExtractor class (=core/windowExtractor.h=). This class has an
=extract= method which returns a WindowsStorage object
(=core/windows.h=) in which windows are stored.
4. To save space consumption, all the reads linked to a given window are
not stored. Only the longer ones are kept. The BinReadStorage class is
used for that purpose (=core/read_storage.h=).
5. In the WindowStorage, we now have the information on the clusters and on
the abundance of each cluster. However we lack a sequence representative
of the cluster. For that purpose the class provides a
=getRepresentativeComputer= method that provides a
KmerRepresentativeComputer (=core/representative.h=). This class can
compute a representative sequence using the (long) reads that were
stored for a given window.
6. The representative can then be segmented to determine what V, D and J
genes are at play. This is done by the FineSegmenter (=core/segment.h=).
* Tests
** Browser
*** Functional
All the browser functional testing is done in the directory
=browser/tests=.
Several stuff must be installed to launch the functional browser
tests. Please see the doc in browser-tests.org.
The functional tests are built using two base files:
- vidjil_browser.rb :: abstracts the vidjil browser (avoid using IDs or
class names that could change in the test). The tests must rely as
much as possible on vidjil_browser. If access to some
data/input/menus are missing they must be addded there.
- browser_test.rb :: prepares the environment for the tests. Each test
file will extend this class (as can be seen in test_multilocus.rb)
The tests are in the files whose name matches the pattern =test*.rb=. The
tests are launched by the script in =launch_functional_tests= which launch
all the files matching the previous pattern. It also backs up the test
reports as =ci_reporter= removes them before each file is run.
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