Merge branch 'vidjil_parser_prototype' of gitlab.inria.fr:vidjil/vidjil into...

Merge branch 'vidjil_parser_prototype' of gitlab.inria.fr:vidjil/vidjil into vidjil_parser_prototype

Merge branch 'vidjil_parser_prototype' of gitlab.inria.fr:vidjil/vidjil into...
Merge branch 'vidjil_parser_prototype' of gitlab.inria.fr:vidjil/vidjil into vidjil_parser_prototype
c09e6d0a · Ryan Herbert · 6a79c7e3 · 2276f061 · c09e6d0a · 6a79c7e3
Commit c09e6d0a authored Aug 07, 2018 by Ryan Herbert
172 changed files
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,12 +16,21 @@ stages:
  - test_functional
  - test_functional_external
  - test_shouldvdj
+  - coverage
  - prepare_release
  - release
  - valgrind_unit
  - valgrind_functional
+  - prepare_deploy
  - deploy_prod

+# Anchors
+
+.coverage_dependency: &lcov_artifact
+  artifacts:
+    paths:
+      - algo/lcov_test_*.filtered
+    expire_in: 6hrs

 # Tools

@@ -36,7 +45,7 @@ test_germlines:
  stage: test_germlines
  script:
    - make -C germline get-all-data
-    - make -C germline/tests
+    - make -C germline tests
  only:
    - /^feature-.*g.*\/.*$/

@@ -45,25 +54,34 @@ test_germlines:

 test_algo_unit:
  stage: test_unit
-  script: make -C algo unit
-  only:
-    - /^feature-.*a.*\/.*$/
-
-test_tools_unit:
-  stage: test_unit
-  script: make -C tools/tests
+  script: make -C algo unit_coverage
+  <<: *lcov_artifact
  only:
    - /^feature-.*a.*\/.*$/

 test_algo_should:
  stage: test_functional
-  script: make -C algo should
+  script: make -C algo should_coverage
  only:
    - /^feature-.*a.*\/.*$/
+  <<: *lcov_artifact

 test_algo_shouldvdj:
  stage: test_shouldvdj
-  script: make -C algo shouldvdj
+  script: make -C algo shouldvdj_coverage
+  <<: *lcov_artifact
+  only:
+    - /^feature-.*a.*\/.*$/
+
+algo_coverage:
+  stage: coverage
+  coverage: /^\s*lines\.*:\s+([0-9.]+\%)/
+  script:
+    - make -C algo lcov_reports
+    - mv algo/reports/ coverage
+  artifacts:
+    paths:
+      - coverage/
  only:
    - /^feature-.*a.*\/.*$/

@@ -101,9 +119,53 @@ release:
    paths:
    - algo/releases/vidjil-algo-`cat algo/release`.tar.gz
    - algo/releases/vidjil-algo-`cat algo/release`/vidjil-algo-`cat algo/release`_`uname -m`
+  allow_failure: false
  tags:
    - ubuntu-16.04-amd64

+copy_release:
+  stage: prepare_deploy
+  script:
+    - |
+      for repo in $ALGO_REPOSITORIES; do
+        echo "Copying release to $repo"
+        scp algo/releases/vidjil-algo*.tar.gz algo/releases/vidjil-algo*/vidjil-algo-*_* $repo
+      done
+      release_name=$(cat algo/release)
+      ssh $VIDJIL_WWW "cd /var/www/html/releases; ln -sf vidjil-algo-${release_name}.tar.gz vidjil-latest.tgz; ln -sf vidjil-algo-${release_name}_x86_64 vidjil-latest_x86_64"
+      ssh $VIDJIL_BONSAI "cd /bio1/www/html/vidjil; scp vidjil-algo-${release_name}* $VIDJIL_BONSAI_PROD:/bio1/www/html/vidjil"
+  only:
+    - /^feature-.*a.*\/release$/
+
+deploy_release_prod:
+  stage: deploy_prod
+  only:
+    - /^feature-.*a.*\/release$/
+  script:
+    - |
+      release_name=$(cat algo/release)
+      ssh $DEPLOY_SERVER "cd releases/vidjil;\
+          tar xvzf vidjil-algo-${release_name}.tar.gz;\
+          make -C vidjil-algo-${release_name};\
+          ln -sfT vidjil-algo-${release_name} next"
+
+test_various_compilers:
+  stage: test_functional
+  only:
+    - feature-a/test-compilers
+  tags:
+    - several-compilers
+  script:
+    - |
+      for CXX in $COMPILERS; do
+        echo "**** Using $CXX for compilation ****"
+        make -C algo clean
+        make -C algo CXX=$CXX unit
+        make -C algo CXX=$CXX should
+        make -C algo CXX=$CXX valgrind_unit
+      done
+
+
 # Client

 test_browser_unit:
@@ -193,6 +255,7 @@ deploy_review:
  stage: deploy_review
  script:
    - make -C browser icons
+    - echo "$REVIEW_CONFIG_JS" > browser/js/conf.js
    - rsync -av --delete browser $DEPLOY_SERVER:$DEPLOY_SERVER_PATH$CI_BUILD_REF_SLUG
  environment:
    name: review/$CI_BUILD_REF_NAME

--- a/.travis.yml
+++ b/.travis.yml
-sudo: false
-
-language: cpp
-compiler: gcc
-
-cache:
-  apt: true
-  pip: true
-
-addons:
- apt:
-   sources:
-   - ubuntu-toolchain-r-test
-   packages:
-   - gcc-4.8
-   - g++-4.8
-   env: COMPILER=g++-4.8
-
-before_install:
-  - export PATH="$HOME/.local/bin:$PATH"
-  - pip install --user cpp-coveralls
-
-before_script: make data ; make germline
-
-script:
-  - export CXX="g++-4.8"
-  - g++ --version
-  - $CXX --version
-  ###
-  - echo '"Build..."' && echo -en 'travis_fold:start:script.build\\r'
-  - make
-  - echo -en 'travis_fold:end:script.build\\r'
-  ###
-  - echo '"Tests, Algo (unit)..."'  && echo -en 'travis_fold:start:script.test-algo-unit\\r'
-  - make unit
-  - echo -en 'travis_fold:end:script.test-algo-unit\\r'
-  ###
-  - echo '"Tests, Algo (functional, .should_get)..."'  && echo -en 'travis_fold:start:script.test-algo-functional\\r'
-  - make COVERAGE=1 should
-  - echo -en 'travis_fold:end:script.test-algo-functional\\r'
-  - make clean
-  ###
-  - echo '"Tests, Algo (functional, .should-vdj.fa)..."'  && echo -en 'travis_fold:start:script.test-algo-functional-vdj\\r'
-  - make shouldvdj
-  - echo -en 'travis_fold:end:script.test-algo-functional-vdj\\r'
-  ###
-  - echo '"Tests, Tools..."'  && echo -en 'travis_fold:start:script.test-tools\\r'
-  - make test_tools
-  - echo -en 'travis_fold:end:script.test-tools\\r'
-  ###
-  - echo '"Tests, Browser (unit)..."'  && echo -en 'travis_fold:start:script.test-browser-unit\\r'
-  - make unit_browser
-  - echo -en 'travis_fold:end:script.test-browser-unit\\r'
-
-after_success:
-  - make should_coveralls COVERALLS_OPTIONS="--gcov /usr/bin/gcov-4.8"
-
-notifications:
-  email:
-    - notifications@vidjil.org
-  webhooks:
-    - https://buildtimetrend.herokuapp.com/travis
--- a/INSTALL.org
+++ b/INSTALL.org
-* Vidjil -- High-throughput Analysis of V(D)J Immune Repertoire
+# Vidjil – High-throughput Analysis of V(D)J Immune Repertoire

-** Algorithm -- Installation instructions
+## Algorithm – Installation instructions

-   #+BEGIN_SRC sh
+``` bash
 make
 ./vidjil-algo -h
-   #+END_SRC
+```

 Detailed compilation, installation and usage instructions
-can be found in [[./doc/algo.org]].
-
+can be found in [./doc/vidjil-algo.md](./doc/vidjil-algo.md).
--- a/Makefile
+++ b/Makefile
@@ -5,6 +5,11 @@ VIDJIL_SERVER_SRC = server/

 TEE = python tools/tee.py -v

+all:
+	$(MAKE) germline
+	$(MAKE) algo
+	$(MAKE) demo
+
 algo:
 	$(MAKE) -C algo


--- a/README.org
+++ b/README.org
-#+TITLE: Vidjil -- High-throughput Analysis of V(D)J Immune Repertoire
-#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)
-
-[[https://travis-ci.org/vidjil/vidjil][https://img.shields.io/travis/vidjil/vidjil/master.svg]]
-[[http://opensource.org/licenses/GPL-3.0][http://img.shields.io/badge/license-GPLv3+-green.svg]]
-[[https://landscape.io/github/vidjil/vidjil][https://landscape.io/github/vidjil/vidjil/master/landscape.svg?style=flat]]
-# https://coveralls.io/r/vidjil/vidjil http://img.shields.io/coveralls/vidjil/vidjil.svg
-
-# Vidjil -- V(D)J recombinations analysis -- [[http://www.vidjil.org]]
-# Copyright (C) 2011-2018 by Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
-# [[contact@vidjil.org]]
+[![](https://gitlab.inria.fr/vidjil/vidjil/badges/dev/build.svg)](https://gitlab.inria.fr/vidjil/vidjil/tree/dev)
+[![](http://img.shields.io/badge/license-GPLv3+-green.svg)](http://opensource.org/licenses/GPL-3.0)
+[<https://landscape.io/github/vidjil/vidjil/master/landscape.svg?style=flat>](https://landscape.io/github/vidjil/vidjil)

 V(D)J recombinations in lymphocytes are essential for immunological
 diversity. They are also useful markers of pathologies, and in
 leukemia, are used to quantify the minimal residual disease during
 patient follow-up.
-High-throughput sequencing (NGS/HTS) now enables the deep sequencing 
-of a lymphoid population with dedicated [[http://omictools.com/rep-seq-c424-p1.html][Rep-Seq]] methods and softwares.
+High-throughput sequencing (NGS/HTS) now enables the deep sequencing
+of a lymphoid population with dedicated [Rep-Seq](http://omictools.com/rep-seq-c424-p1.html) methods and softwares.

-The Vidjil platform contains three components. 
-Vidjil-algo processes high-througput sequencing data to *extract V(D)J
-junctions and gather them into clones*. Vidjil-algo starts 
+The Vidjil platform contains three components.
+Vidjil-algo processes high-througput sequencing data to **extract V(D)J
+junctions and gather them into clones**. Vidjil-algo starts
 from a set of reads and detects "windows" overlapping the actual CDR3.
 This is based on an fast and reliable seed-based heuristic and allows
 to output all sequenced clones. The analysis is extremely fast
 because, in the first phase, no alignment is performed with database
-germline sequences. 
+germline sequences.

-The Vidjil *web application* is made for the interactive visualization and
+The Vidjil **web application** is made for the interactive visualization and
 analysis of clones and their tracking along the time in a MRD setup or
 in a immunological study. The web application can visualize data processed by
 the Vidjil algorithm or by other V(D)J analysis pipelines, and
 enables to explore further cluterings proposed
 by software and/or done manually done by the user.
-The web application can be linked to a *sample, experiment and patient database*
+The web application can be linked to a **sample, experiment and patient database**
 able to store sequencing data and metadata, to run RepSeq software
 and to save annotations directly from the web application, with authentication.
 Clinicians or researchers in immunology or hematology
 can manage, upload, analyze and annotate their runs directly on the web applicaiton.

-* Vidjil components
+# Vidjil components

-** Vidjil-algo
+## Vidjil-algo

- Stable releases can be downloaded from http://bioinfo.lille.inria.fr/vidjil
- Development code is under [[algo/]]
- Documentation, compilation and installation instructions: [[doc/algo.org]]
+  - Stable releases can be downloaded from <http://bioinfo.lille.inria.fr/vidjil> and <http://www.vidjil.org/releases>
+  - Development code is under *algo/*
+  - Documentation, compilation and installation instructions: *doc/vidjil-algo.md*

-** The web application
+## The web application

- Access at https://app.vidjil.org/ (demo login: demo@vidjil.org, password: vidjil)
- Please contact us if you would like to test your data and have a full account on the web server
- Development code is under [[browser/]] and [[server/]] (a =make= in those directories
-  will get the necessary files)
- Documentation is in [[doc/]], it is also available from [[http://www.vidjil.org/doc]]
+  - Access at <https://app.vidjil.org/> (demo login: demo@vidjil.org, password: vidjil)
+  - Please contact us if you would like to test your data and have a full account on the web server
+  - Development code is under *browser/* and *server/* (a `make` in those directories
+    will get the necessary files)
+  - Documentation is in *doc/*, it is also available from <http://www.vidjil.org/doc>

-* Code and license
+# Code and license

-Vidjil is open-source, released under GNU GPLv3 license. 
-You are welcome to redistribute it under [[http://git.vidjil.org/blob/master/doc/LICENSE][certain conditions]]. 
+Vidjil is open-source, released under GNU GPLv3 license.
+You are welcome to redistribute it under [certain conditions](http://git.vidjil.org/blob/master/doc/LICENSE).
 This software is for research use only and comes with no warranty.

-The development code is available on [[http://git.vidjil.org/]].
+The development code is available on <http://gitlab.vidjil.org/>.
 Bug reports, issues and patches are welcome.

-* Donations
+# Donations

-We welcome Bitcoin donations to [[bitcoin:13u12m6LxVhesKEpS6T5wpYN19LHpwk8xt][13u12m6LxVhesKEpS6T5wpYN19LHpwk8xt]].
-Thank you for your support !
+We welcome Bitcoin donations to [13u12m6LxVhesKEpS6T5wpYN19LHpwk8xt](bitcoin:13u12m6LxVhesKEpS6T5wpYN19LHpwk8xt).
+Thank you for your support \!

-* The Vidjil team
+# The Vidjil team

-Vidjil is developed by Aurélien Béliard, [[http://cristal.univ-lille.fr/~giraud][Mathieu Giraud]], Ryan Herbert, Tatiana Rocher and [[http://cristal.univ-lille.fr/~salson][Mikaël Salson]]
-from the [[http://cristal.univ-lille.fr/bonsai][Bonsai bioinformatics team]] (CRIStAL, CNRS, U. Lille, Inria Lille).
+Vidjil is developed by Aurélien Béliard, [Mathieu Giraud](http://cristal.univ-lille.fr/~giraud), Ryan Herbert, Tatiana Rocher and [Mikaël Salson](http://cristal.univ-lille.fr/~salson)
+from the [Bonsai bioinformatics team](http://cristal.univ-lille.fr/bonsai) (CRIStAL, CNRS, U. Lille, Inria Lille).
 Vidjil is also developed by external colleagues:
 Marc Duez located in Bristol (School of Social and Community Medicine, University of Bristol)
 and Florian Thonier located in Rennes (department of hematology)
-Vidjil is developed in collaboration with 
-the [[http://biologiepathologie.chru-lille.fr/organisation-fbp/91210.html][department of Hematology]] of CHRU Lille, 
-the [[http://www.ircl.org/plate-forme-genomique.html][Functional and Structural Genomic Platform]] (U. Lille 2, IFR-114, IRCL), 
-and the [[http://www.euroclonality.org/][EuroClonality-NGS]] working group.
+Vidjil is developed in collaboration with
+the [department of Hematology](http://biologiepathologie.chru-lille.fr/organisation-fbp/91210.html) of CHRU Lille,
+the [Functional and Structural Genomic Platform](http://www.ircl.org/plate-forme-genomique.html) (U. Lille 2, IFR-114, IRCL),
+and the [EuroClonality-NGS](http://www.euroclonality.org/) working group.
 The research is supported by SIRIC ONCOLille (Grant INCa-DGOS-Inserm 6041), by Région Nord-Pas-de-Calais/Hauts-de-France (ABILES),
 by Inria and by InCA.

-* References
+# References

 If you use Vidjil for your research, please cite the following references:

 Marc Duez et al.,
 “Vidjil: A web platform for analysis of high-throughput repertoire sequencing”,
 PLOS ONE 2016, 11(11):e0166126
-http://dx.doi.org/10.1371/journal.pone.0166126
+<http://dx.doi.org/10.1371/journal.pone.0166126>

 Mathieu Giraud, Mikaël Salson, et al.,
 “Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing”,
-BMC Genomics 2014, 15:409 
-[[http://dx.doi.org/10.1186/1471-2164-15-409]]
+BMC Genomics 2014, 15:409
+<http://dx.doi.org/10.1186/1471-2164-15-409>

 You may also be interested in the following publication for the diagnosis of
 acute lymphoblastic leukemia with high-throughput sequencing:
@@ -102,4 +94,4 @@ acute lymphoblastic leukemia with high-throughput sequencing:
 Yann Ferret, Aurélie Caillault, et al., “Multi-loci diagnosis of acute
 lymphoblastic leukaemia with high-throughput sequencing and bioinformatics
 analysis”, British Journal of Haematology 2016
-http://dx.doi.org/10.1111/bjh.13981
+<http://dx.doi.org/10.1111/bjh.13981>
--- a/algo/Makefile
+++ b/algo/Makefile
@@ -6,9 +6,19 @@ else
 	COVERAGE_OPTION=
 endif

+ifeq ($(CXXFLAGS), )
+  CXXFLAGS := -W -Wall -std=c++11 -O2 -DNDEBUG
+endif
+override CXXFLAGS += $(COVERAGE_OPTION) $(DEBUG)
+ifeq ($(LDFLAGS),)
+  LDFLAGS := $(COVERAGE_OPTION)
+endif
+COV_OUTFILE?=lcov.out
+BASE_PATH=$(dir $(abspath .))

-OPTIM=-O2 -DNDEBUG  $(COVERAGE_OPTION) $(DEBUG)
-override CXXFLAGS += -W -Wall -std=c++11 $(OPTIM)
+export CXXFLAGS
+export LDFLAGS
+export CXX

 ## inspired from http://stackoverflow.com/questions/399850/best-compiler-warning-level-for-c-c-compilers/401276
 PARANOID= -Wall -Weffc++ -pedantic  \
@@ -50,7 +60,7 @@ CREATE_VERSION_GIT_H := $(shell test -x ./create-git-version-h.sh && ./create-gi

 TEE = python ../tools/tee.py -v

-.PHONY: all core lib clean forcedep
+.PHONY: all core lib clean forcedep gcovr_reports

 all: $(VIDJIL) $(ALIGN_CGI) $(SIMILARITY_CGI) $(SIMILARITY_TOOL)
 	$(MAKE) -C $(TOOLDIR)
@@ -63,7 +73,7 @@ static:
 ###

 paranoid: clean
-	$(MAKE) vidjil OPTIM="$(PARANOID)"
+	$(MAKE) vidjil CXXFLAGS="$(CXXFLAGS) $(PARANOID)"

 ###

@@ -91,17 +101,17 @@ cleanspaced:

 $(ALIGN_CGI): cgi/align.o $(LIBCORE)
 	mkdir -p $(CGIDIR)
-	$(MAKE) -C core OPTIM="$(OPTIM)"
+	$(MAKE) -C core
 	$(CXX) -o $@ $^ $(LDFLAGS) $(LDLIBS) $(CXXFLAGS)

 $(SIMILARITY_CGI): cgi/similarity.o $(LIBCORE)
 	mkdir -p $(CGIDIR)
-	$(MAKE) -C core OPTIM="$(OPTIM)"
+	$(MAKE) -C core
 	$(CXX) -o $@ $^ $(LDFLAGS) $(LDLIBS) $(CXXFLAGS)

 $(SIMILARITY_TOOL): cgi/similarity.o $(LIBCORE)
 	mkdir -p $(TOOLDIR)
-	$(MAKE) -C core OPTIM="$(OPTIM)"
+	$(MAKE) -C core
 	$(CXX) -o $@ $^ $(LDFLAGS) $(LDLIBS) $(CXXFLAGS)

 ###
@@ -111,9 +121,9 @@ debug:
 	$(MAKE) DEBUG="-ggdb"

 $(VIDJIL): $(BINDIR)%: $(MAIN).o $(LIBCORE)
-	$(MAKE) -C core OPTIM="$(OPTIM)"
-	$(MAKE) -C lib OPTIM="$(OPTIM)"
-	$(CXX) -o $@ $^ $(LDFLAGS) $(LDLIBS) $(CXXFLAGS)
+	$(MAKE) -C core
+	$(MAKE) -C lib
+	$(CXX) -o $@ $^ $(LDFLAGS) $(LDLIBS)

 ###
 # Subdirectories
@@ -146,7 +156,7 @@ cleanall: cleancoverage

 test:
 	$(MAKE) -C tests cleantests
-	$(TEE) '$(MAKE) COVERAGE="$(COVERAGE)" unit' tests/out-unit.log
+	$(TEE) '$(MAKE) unit' tests/out-unit.log
 	$(MAKE) functional
 	@echo
 	@echo "*** All tests passed. Congratulations !"
@@ -160,24 +170,27 @@ snapshot_diff:
 snapshot_diff_current:
 	$(MAKE) -C tests snapshot_diff_current

-unit: all
+unit:
+	$(MAKE) CXXFLAGS="$(filter-out -DNDEBUG, $(CXXFLAGS))" all
 	@echo "*** Launching unit tests..."
-	$(MAKE) COVERAGE="$(COVERAGE_OPTION)" -C tests
+	$(MAKE) -C tests
 	@echo "*** All unit tests passed"

-functional: all
+functional:
 	$(TEE) '$(MAKE) should'      tests/out-should-get.log
 	$(TEE) '$(MAKE) shouldvdj'   tests/out-should-vdj.log

-should: all
+should:
+	$(MAKE) CXXFLAGS="$(filter-out -DNDEBUG, $(CXXFLAGS))" all
 	@echo
 	@echo "*** Launching .should_get tests..."
-	$(MAKE) COVERAGE="$(COVERAGE_OPTION)" -C tests should
+	$(MAKE) -C tests should
 	@echo "*** All .should_get tests passed"

-shouldvdj: all
+shouldvdj:
 	@echo
-	$(MAKE) COVERAGE="$(COVERAGE_OPTION)" -C tests shouldvdj_if_python
+	$(MAKE) CXXFLAGS="$(filter-out -DNDEBUG, $(CXXFLAGS))" all
+	$(MAKE) -C tests shouldvdj_if_python


 valgrind_unit:
@@ -192,27 +205,29 @@ valgrind_should:

 coverage: unit_coverage should_coverage

-unit_coverage: clean
+unit_coverage: cleancoverage
 	$(MAKE) COVERAGE=1 unit
-should_coverage: clean
+	$(MAKE) COV_OUTFILE=lcov_test_unit gencov
+should_coverage: cleancoverage
+	$(MAKE) COVERAGE=1 should
+	$(MAKE) COV_OUTFILE=lcov_test_should gencov
+shouldvdj_coverage: cleancoverage
+	$(MAKE) COVERAGE=1 shouldvdj
+	$(MAKE) COV_OUTFILE=lcov_test_shouldvdj gencov
+functional_coverage: cleancoverage
 	$(MAKE) COVERAGE=1 functional
+	$(MAKE) COV_OUTFILE=lcov_test_functional gencov

-### Reports with gcovr
-
-unit_gcovr: unit_coverage
-	mkdir -p reports
-	which gcovr > /dev/null && (gcovr -r . -e tests/ --xml > ../reports/unit_coverage.xml) || echo "gcovr is needed to generate a full report"
-should_gcovr: should_coverage
-	mkdir -p reports
-	which gcovr > /dev/null && (gcovr -r . -e tests/ --xml > ../reports/should_coverage.xml) || echo "gcovr is needed to generate a full report"
+gencov:
+	which lcov > /dev/null || exit 0
+	lcov --rc geninfo_adjust_src_path="$(BASE_PATH)" -d . -c -o $(COV_OUTFILE)
+	lcov  --remove $(COV_OUTFILE) '/usr/*' '*algo/tests/*' '*algo/lib/*' '*algo/tools/*' -o $(COV_OUTFILE).filtered

-### Upload to coveralls.io
-
-unit_coveralls:
-	coveralls $(COVERALLS_OPTIONS) --exclude release --exclude lib --exclude tests --exclude tools --exclude tests --exclude ../tools --exclude lib --gcov-options '\-lp'
-should_coveralls:
-	coveralls $(COVERALLS_OPTIONS) --exclude release --exclude lib --exclude tests --exclude tools --exclude tests --exclude ../tools --exclude lib --gcov-options '\-lp' -r algo
+### Reports with lcov

+lcov_reports:
+	mkdir -p reports
+	which lcov > /dev/null && (lcov $(addprefix -a ,$(wildcard lcov*.filtered)) | sed 's_^SF:algo_SF:'"$(BASE_PATH)"'/algo_' > lcov_filtered_total.out && genhtml --branch-coverage --legend --output-directory reports/ lcov_filtered_total.out ) || echo "gcovr is needed to generate a full report"

 ### cppcheck

@@ -261,9 +276,9 @@ RELEASE_DIR_TMP = releases/tmp
 RELEASE_ALGO = src/
 RELEASE_TOOLS = $(wildcard ../tools/*.py)
 RELEASE_MAKE = ../tools/tests/Makefile ../doc/Makefile
-RELEASE_TESTS = ../doc/format-analysis.org $(wildcard ../doc/analysis-example.vidjil) $(wildcard ../tools/tests/*.should_get) ../tools/tests/should-to-tap.sh ../tools/diff_json.sh ../demo/get-sequences ../demo/Demo-X5.fa ../demo/Makefile
-RELEASE_GERMLINES = ../germline/Makefile ../germline/germline_id ../germline/get-saved-germline ../germline/get-germline ../germline/split-from-imgt.py $(wildcard ../germline/*.g) ../germline/revcomp-fasta.py ../germline/fasta.py
-RELEASE_HELP = ../doc/algo.org ../doc/locus.org ../doc/dev.org ../doc/should-vdj.org ../doc/credits.org ../doc/CHANGELOG ../doc/LICENSE ../README.org ../INSTALL.org
+RELEASE_TESTS = ../doc/vidjil-format.md $(wildcard ../doc/analysis-example.vidjil) $(wildcard ../tools/tests/*.should_get) ../tools/should.py  ../tools/diff_json.sh ../demo/get-sequences ../demo/Demo-X5.fa ../demo/Makefile
+RELEASE_GERMLINES = ../germline/Makefile ../germline/germline_id ../germline/get-saved-germline ../germline/get-germline ../germline/split-from-imgt.py $(wildcard ../germline/*.g) ../germline/revcomp-fasta.py ../germline/fasta.py ../germline/homo-sapiens/IKZF*fa ../germline/homo-sapiens/ERG*fa 
+RELEASE_HELP = ../doc/vidjil-algo.md ../doc/locus.md ../doc/dev.org ../doc/should-vdj.org ../doc/credits.md ../doc/CHANGELOG ../doc/LICENSE ../README.md ../INSTALL.md
 RELEASE_FILES = $(RELEASE_TOOLS) $(RELEASE_TESTS) $(RELEASE_MAKE) $(RELEASE_GERMLINES) $(RELEASE_HELP)


@@ -297,7 +312,7 @@ release_create:
 	for file in $(RELEASE_FILES); do\
 	  dir=$(RELEASE_DIR_TMP)/$(RELEASE_NAME)/algo/`dirname "$$file"`/;    \
 	  mkdir -p $$dir; \
-	  cp -v "$$file" $$dir/;     \
+	  cp -v "$$file" $$dir/ || exit 1;     \
 	done

 	# A spurious algo/ directory is created, remove it

--- a/algo/core/Makefile
+++ b/algo/core/Makefile
 CXX?=g++
-OPTIM=-O2 
-override CXXFLAGS += -W -Wall -std=c++11 $(OPTIM)
+ifeq ($(CXXFLAGS), )
+  CXXFLAGS := -W -Wall -std=c++11 -O2 -DNDEBUG
+endif
+export CXXFLAGS
 INC=-I ../
 SRCCORE=$(wildcard *.cpp)
 OBJCORE=$(SRCCORE:.cpp=.o)

--- a/algo/core/affectanalyser.cpp
+++ b/algo/core/affectanalyser.cpp
@@ -140,6 +140,8 @@ affect_infos KmerAffectAnalyser::getMaximum(const KmerAffect &before,
  results.first_pos_max = results.last_pos_max = 0;
  results.nb_before_left = results.nb_before_right = results.nb_after_right = results.nb_after_left = 0;
  currentValue = 0;
+  int nb_during_max = 0;
+  bool continue_max;

  for (int i = 0; i < min(length,span - maxOverlap); i++) {
    if (affectations[i] == after) {
@@ -151,7 +153,8 @@ affect_infos KmerAffectAnalyser::getMaximum(const KmerAffect &before,
  for (int i = span - maxOverlap; i < length; i++) {
    /* i - span + maxOverlap, to avoir overlapping k-mers */

-
+    continue_max = false;
+    
    /* Read the current affectations, and store them both in currentValue and at the right of the previous maximum.
       The affectation of 'before' is interpreted relatively to span and maxOverlap */

@@ -168,18 +171,39 @@ affect_infos KmerAffectAnalyser::getMaximum(const KmerAffect &before,

    /* If we raise above the max, or if we continue a previous maximum (even from a distant position), store in results */
    if (currentValue >= results.max_value) {
-      if (currentValue > results.max_value)
+      if (currentValue > results.max_value) {
        results.first_pos_max = i;
+
+        // We are above the previous max. We reaffect the ignored affectations
+        // during the previous plateau.
+        results.nb_after_left += nb_during_max;
+        results.nb_before_left += nb_during_max;
+        nb_during_max = 0;
+      } else if (results.last_pos_max == i - 1) {
+        if (affectations[i] == after) {
+          // in such a case we also have affectations[i - span + maxOverlap] == before
+          // because we are still on a maximum this means currentValue hasn't changed
+          assert (affectations[i - span + maxOverlap] == before);
+          nb_during_max++;
+          continue_max = true;
+        }
+      }
      results.max_value = currentValue;
      results.last_pos_max = i;

-      /* What was at the right of the previous maximum is now at the left of the current maximum */
-      results.nb_after_left += results.nb_after_right;
-      results.nb_before_left += results.nb_before_right;
+      if (! continue_max) {
+        /* What was at the right of the previous maximum is now at the left of
+         * the current maximum.  But we only count them if we are not on a
+         * plateau. If we later reach a higher maximum they will be counted
+         * back (see above) */
+        results.nb_after_left += results.nb_after_right;
+        results.nb_before_left += results.nb_before_right;
+      }
      results.nb_after_right = 0;
      results.nb_before_right = 0;
    }

+
 #ifdef DEBUG_GET_MAXIMUM
    cout << setw(3) << i
         << "  " << affectations[i - span + maxOverlap] << ((affectations[i - span + maxOverlap] == before)?"!":" ")

--- a/algo/core/affectanalyser.h
+++ b/algo/core/affectanalyser.h
@@ -22,15 +22,25 @@ typedef enum affect_options_e {
 } affect_options_t;


-/* Stores results during .getMaximum() computation */
+/*