vidjil.cpp: Use set_index for setting the Germline index

set_index() keeps track of the number of germlines refeering to it.
This is necessary so that the last germline destructor can actually
delete the index.
8 jobs for feature-a/fix_valgrind_issues in 53 minutes and 18 seconds (queued for 2 seconds)
Status Job ID Name Coverage
  Test Tools
passed #61009
test_tools

00:00:05

 
  Test Unit
passed #61010
test_algo_unit

00:01:44

passed #61011
test_tools_unit

00:00:05

 
  Test Functional
passed #61012
test_algo_should

00:07:55

 
  Test Shouldvdj
passed #61013
test_algo_shouldvdj

00:09:15

 
  Prepare Release
failed #61014
allowed to fail manual
prepare_release

00:01:32

 
  Valgrind Unit
passed #61015
valgrind
algo_valgrind_unit

00:02:56

 
  Valgrind Functional
passed #61016
valgrind manual
algo_valgrind_functional

00:29:50

 
Name Stage Failure
failed
prepare_release Prepare Release There is an unknown failure, please try again
make[2]: *** [Stanford_S22.fasta] Error 2
make[2]: Leaving directory '/home/gitlab-runner/builds/b8d876c1/0/vidjil/vidjil/algo/releases/vidjil-rc/src/tests/data'
Makefile:18: recipe for target 'test' failed
make[1]: *** [test] Error 2
make[1]: Leaving directory '/home/gitlab-runner/builds/b8d876c1/0/vidjil/vidjil/algo/releases/vidjil-rc'
Makefile:317: recipe for target 'release_check' failed
make: *** [release_check] Error 2
make: Leaving directory '/home/gitlab-runner/builds/b8d876c1/0/vidjil/vidjil/algo'
ERROR: Job failed: exit status 1