Commit 54946cae authored by Mathieu Giraud's avatar Mathieu Giraud

core/germline.h, vidjil.cpp: rename and better define 'xxx' and 'zzz' pseudo-germlines

parent 39777068
......@@ -24,6 +24,11 @@ enum SEGMENTATION_METHODS {
#define CYS104_IN_GAPPED_V 310 // First nucleotide of Cys104
#define PHE118_TRP118_IN_GAPPED_J 38 // Last nucleotide of Phe118/Trp118
#define PSEUDO_UNEXPECTED "unexpected"
#define PSEUDO_UNEXPECTED_CODE 'x'
#define PSEUDO_NOT_ANALYZED "not analyzed"
#define PSEUDO_NOT_ANALYZED_CODE 'z'
using namespace std;
using json = nlohmann::json;
......
......@@ -883,16 +883,16 @@ int main (int argc, char **argv)
}
if (multi_germline_unexpected_recombinations_12) {
Germline *pseudo = new Germline("xxx", 'x', -10, "", trim_sequences);
Germline *pseudo = new Germline(PSEUDO_UNEXPECTED, PSEUDO_UNEXPECTED_CODE, -10, "", trim_sequences);
pseudo->seg_method = SEG_METHOD_MAX12 ;
pseudo->index = multigermline->index ;
multigermline->germlines.push_back(pseudo);
}
if (multi_germline_unexpected_recombinations_1U) {
Germline *pseudo_u = new Germline("xxx", 'x', -10, "", trim_sequences);
Germline *pseudo_u = new Germline(PSEUDO_UNEXPECTED, PSEUDO_UNEXPECTED_CODE, -10, "", trim_sequences);
pseudo_u->seg_method = SEG_METHOD_MAX1U ;
// TODO: there should be more up/downstream regions for the 'yyy' germline. And/or smaller seeds ?
// TODO: there should be more up/downstream regions for the PSEUDO_UNEXPECTED germline. And/or smaller seeds ?
pseudo_u->index = multigermline->index ;
multigermline->germlines.push_back(pseudo_u);
}
......@@ -1601,7 +1601,7 @@ int main (int argc, char **argv)
int nb_segmented = 0 ;
map <string, int> nb_segmented_by_germline ;
Germline *not_segmented = new Germline("zzz", 'z', 0);
Germline *not_segmented = new Germline(PSEUDO_NOT_ANALYZED, PSEUDO_NOT_ANALYZED_CODE, 0);
while (reads->hasNext())
{
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment