Commit 7f08921e authored by Mathieu Giraud's avatar Mathieu Giraud

core/{tools,germline}.{h,cpp}: move seedMap to tools.cpp

See #3293.
parent a02ec14d
...@@ -353,13 +353,7 @@ void MultiGermline::build_from_json(string path, string json_filename_and_filter ...@@ -353,13 +353,7 @@ void MultiGermline::build_from_json(string path, string json_filename_and_filter
break ; break ;
} }
map<string, string> seedMap; seed = (default_seed.size() == 0) ? seed : default_seed;
seedMap["13s"] = SEED_S13;
seedMap["12s"] = SEED_S12;
seedMap["10s"] = SEED_S10;
seedMap["9s"] = SEED_9;
seed = (default_seed.size() == 0) ? seedMap[seed] : default_seed;
//for each set of recombination 3/4/5 //for each set of recombination 3/4/5
for (json::iterator it2 = recom.begin(); it2 != recom.end(); ++it2) { for (json::iterator it2 = recom.begin(); it2 != recom.end(); ++it2) {
......
...@@ -15,8 +15,6 @@ ...@@ -15,8 +15,6 @@
#include "filter.h" #include "filter.h"
#include <climits> #include <climits>
#define DEFAULT_GERMLINE_SEED SEED_S10
enum SEGMENTATION_METHODS { enum SEGMENTATION_METHODS {
SEG_METHOD_53, // Regular or incomplete germlines, 5'-3' SEG_METHOD_53, // Regular or incomplete germlines, 5'-3'
SEG_METHOD_543, // Regular or incomplete germlines, 5'-3', with an additional middle gene (such a D gene) SEG_METHOD_543, // Regular or incomplete germlines, 5'-3', with an additional middle gene (such a D gene)
......
...@@ -19,6 +19,13 @@ int seed_weight(const string &seed) ...@@ -19,6 +19,13 @@ int seed_weight(const string &seed)
return count(seed.begin(), seed.end(), SEED_YES); return count(seed.begin(), seed.end(), SEED_YES);
} }
map<string, string> seedMap = {
{"9c", "#########"},
{"10s", "#####-#####"},
{"12s", "######-######"},
{"13s", "#######-######"}
};
char spaced_buf[MAX_SEED_SIZE+1]; char spaced_buf[MAX_SEED_SIZE+1];
string spaced(const string &input, const string &seed) { string spaced(const string &input, const string &seed) {
......
...@@ -43,16 +43,12 @@ using namespace std; ...@@ -43,16 +43,12 @@ using namespace std;
#define PRINT_VAR(v) cerr << #v << " = " << v << endl #define PRINT_VAR(v) cerr << #v << " = " << v << endl
#define NB_N_CHOOSE_K_STORED 500
#define SEED_YES '#' #define SEED_YES '#'
// Common seeds // Common seeds
#define SEED_9 "#########" extern map<string, string> seedMap;
#define SEED_S10 "#####-#####"
#define SEED_S12 "######-######"
#define SEED_S13 "#######-######"
#define NB_N_CHOOSE_K_STORED 500
string seed_contiguous(int k); string seed_contiguous(int k);
......
...@@ -106,7 +106,6 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ; ...@@ -106,7 +106,6 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define DEFAULT_K 0 #define DEFAULT_K 0
#define DEFAULT_W 50 #define DEFAULT_W 50
#define DEFAULT_SEED DEFAULT_GERMLINE_SEED
#define DEFAULT_MAX_AUDITIONED 2000 #define DEFAULT_MAX_AUDITIONED 2000
#define DEFAULT_RATIO_REPRESENTATIVE 0.5 #define DEFAULT_RATIO_REPRESENTATIVE 0.5
......
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