Commit 9402d384 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil-algo: (non-)release 2018.10, will be tagged as 2018.10-dev

This release does not work on some systems.
See #3601 and #3602.
parent be790379
Pipeline #47721 failed with stages
in 26 minutes and 36 seconds
...@@ -10,6 +10,7 @@ This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil pla ...@@ -10,6 +10,7 @@ This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil pla
* New AIRR .tsv output (core/output.c) #2828 * New AIRR .tsv output (core/output.c) #2828
* Updated documentation * Updated documentation
* New and updated unit and functional tests * New and updated unit and functional tests
* Known regressions: This version may not work on some systems #3601 #3602
2018-07-18 The Vidjil Team 2018-07-18 The Vidjil Team
* Cleaned memory after the heuristic, lowering memory usage up to 50% on datasets with many 1-read clones #2120 #3387 * Cleaned memory after the heuristic, lowering memory usage up to 50% on datasets with many 1-read clones #2120 #3387
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# vidjil-algo 2018.10 # vidjil-algo 2018.10-dev
**Command-line manual** **Command-line manual**
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)* *The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)*
...@@ -70,6 +70,8 @@ Vidjil-algo has been successfully tested on the following platforms : ...@@ -70,6 +70,8 @@ Vidjil-algo has been successfully tested on the following platforms :
- Ubuntu 18.04 LTS - Ubuntu 18.04 LTS
- OS X 10.9, 10.10, 10.11 - OS X 10.9, 10.10, 10.11
Use Vidjil-algo 2018.07.2 for a wide support of these platforms.
Vidjil-algo is developed with continuous integration using systematic unit and functional testing. Vidjil-algo is developed with continuous integration using systematic unit and functional testing.
The development team internally uses [Gitlab CI](http://gitlab.vidjil.org/pipelines) and [Jenkins](https://jenkins-ci.org/) for that. The development team internally uses [Gitlab CI](http://gitlab.vidjil.org/pipelines) and [Jenkins](https://jenkins-ci.org/) for that.
...@@ -82,7 +84,9 @@ To compile Vidjil-algo, make sure: ...@@ -82,7 +84,9 @@ To compile Vidjil-algo, make sure:
- to be on a POSIX system ; - to be on a POSIX system ;
- to have a C++11 compiler (as `g++` 4.8 or above, `g++` 7.3 being supported, or `clang` 3.3 or above). - to have a C++11 compiler (as `g++` 4.8 or above, `g++` 7.3 being supported, or `clang` 3.3 or above).
This version of Vidjil-algo does not work with `g++` 8.0 or above. Note that the 2018.10-dev version of Vidjil-algo does not work with `g++` 8.0 or above and with `clang`.
Use the 2018.07.2 version for a wider support.
- to have the `zlib` installed (`zlib1g-dev` package under Debian/Ubuntu, - to have the `zlib` installed (`zlib1g-dev` package under Debian/Ubuntu,
`zlib-devel` package under Fedora/CentOS). `zlib-devel` package under Fedora/CentOS).
...@@ -637,7 +641,7 @@ For example `-uu -X 1000` splits the unsegmented reads from the 1000 first reads ...@@ -637,7 +641,7 @@ For example `-uu -X 1000` splits the unsegmented reads from the 1000 first reads
## AIRR .tsv output ## AIRR .tsv output
Since version 2018.10, vidjil-algo supports the [AIRR format](http://docs.airr-community.org/en/latest/datarep/rearrangements.html#fields). Since version 2018.10-dev, vidjil-algo supports the [AIRR format](http://docs.airr-community.org/en/latest/datarep/rearrangements.html#fields).
We export all required fields, some optional fields, as also some custom fields (+). We export all required fields, some optional fields, as also some custom fields (+).
Note that Vidjil-algo is designed to efficiently gather reads from large datasets into clones. Note that Vidjil-algo is designed to efficiently gather reads from large datasets into clones.
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