On séquence directement NA12878 -> inutile pour le pipeline seul
**** TODO Tester seul la partie bioinformatique
   Tout résumé ici : https://www.nist.gov/programs-projects/genome-bottle
- methode https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/analysis/Illumina_PlatinumGenomes_NA12877_NA12878_09162015/IlluminaPlatinumGenomes-user-guide.pdf
- vcf
     https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/latest/GRCh38/
NB: à quoi correspond https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/analysis/Illumina_PlatinumGenomes_NA12877_NA12878_09162015/hg38/2.0.1/NA12878/ ??
   Article comparant les variant calling : https://www.biorxiv.org/content/10.1101/2020.12.11.422022v1.full.pdf
   Article pour vcfeval : https://www.nature.com/articles/s41587-019-0054-x

**** TODO Tester seul la partie bioinformatique
- methode https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/analysis/Illumina_PlatinumGenomes_NA12877_NA12878_09162015/IlluminaPlatinumGenomes-user-guide.pdf
- vcf
     https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/latest/GRCh38/

NB: à quoi correspond https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/analysis/Illumina_PlatinumGenomes_NA12877_NA12878_09162015/hg38/2.0.1/NA12878/ ??

*** TODO Hap.py

Patch
#+begin_src diff
--- CMakeLists.txt.orig	2023-02-01 23:55:18.171758209 +0100
+++ CMakeLists.txt	2023-02-01 23:07:43.945491855 +0100
@@ -23,25 +23,25 @@
     set (VCFEVAL_AVAILABLE 0)
 endif()

-execute_process(
-    COMMAND ${CMAKE_SOURCE_DIR}/external/make_dependencies.sh
-    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-    RESULT_VARIABLE EXTERNAL_SUCCESS)
-
-if(NOT "${EXTERNAL_SUCCESS}" STREQUAL "0")
-    message(FATAL_ERROR "Building external dependencies has failed")
-endif()
-
-set(Boost_USE_STATIC_LIBS        ON)  # only find static libs
-set(Boost_USE_MULTITHREADED      ON)
-set(Boost_USE_STATIC_RUNTIME     ON)
+#execute_process(
+#    COMMAND ${CMAKE_SOURCE_DIR}/external/make_dependencies.sh
+#    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+#    RESULT_VARIABLE EXTERNAL_SUCCESS)
+
+#if(NOT "${EXTERNAL_SUCCESS}" STREQUAL "0")
+#    message(FATAL_ERROR "Building external dependencies has failed")
+#endif()
+
+#set(Boost_USE_STATIC_LIBS        ON)  # only find static libs
+#set(Boost_USE_MULTITHREADED      ON)
+#set(Boost_USE_STATIC_RUNTIME     ON)
 # un-break library finding
-set(Boost_NO_BOOST_CMAKE         ON)
-set(Boost_NO_SYSTEM_PATHS        ON)
+#set(Boost_NO_BOOST_CMAKE         ON)
+#set(Boost_NO_SYSTEM_PATHS        ON)
-set(BOOST_ROOT ${CMAKE_BINARY_DIR})
-message("Using our own Boost, which was built at ${HAPLOTYPES_SOURCE_DIR}/external/boost_install")
+#set(BOOST_ROOT ${CMAKE_BINARY_DIR})
+#message("Using our own Boost, which was built at ${HAPLOTYPES_SOURCE_DIR}/external/boost_install")
 find_package(Boost 1.55.0 COMPONENTS thread iostreams regex unit_test_framework filesystem system program_options REQUIRED)
 include_directories(${Boost_INCLUDE_DIRS})
#+end_src

Il faut rajouter dans Roc.cpp
#include <stdexcept>
#include <limits>

Patch Roc.cpp
#+begin_src diff
--- src/c++/lib/tools/Roc.cpp.orig	2023-02-01 23:52:50.514230141 +0100
+++ src/c++/lib/tools/Roc.cpp	2023-02-01 23:52:52.729223136 +0100
@@ -34,6 +34,9 @@
  */

 #include "helpers/Roc.hh"
+#include <stdexcept>
+#include <limits>
+
 #include <algorithm>
 #include <cmath>
#+end_src