1 files changed, 91 insertions, 0 deletions
diff --git a/biology/phrap/files/patch-pairs.c b/biology/phrap/files/patch-pairs.c
new file mode 100644
index 000000000000..d81b915fda34
--- /dev/null
+++ b/biology/phrap/files/patch-pairs.c
@@ -0,0 +1,91 @@
+--- ./pairs.c.orig	2009-04-23 00:12:20.000000000 +0200
++++ ./pairs.c	2014-08-02 12:39:30.000000000 +0200
+@@ -37,6 +37,16 @@
+ int single_domain;
+ double mask_frac;
+ 
++void revise_qd_scores(Query_domain *);
++void visit_cand_pairs_scores( Cand_pair *);
++void merge_qds(Database *, int);
++void init_qd_trims(Query_domain *);
++void test_qd1_merges(Query_domain *, Query_domain *);
++void test_qd2_merges(Query_domain *, Query_domain *);
++void compare_query_domains(Query_domain *, Query_domain *);
++void print_score_list(int, Query_domain *);
++void print_pair(Aligned_pair *, FILE *, int);
++
+ set_domain_vars()
+ {
+   single_domain = parameters->masklevel == 0 || parameters->masklevel == 101;
+@@ -697,6 +707,7 @@
+ 																						  */
+ }
+ 
++void
+ visit_cand_pairs_scores(cand_pair)
+      Cand_pair *cand_pair;
+ {
+@@ -1423,6 +1434,7 @@
+ 
+ int trim_flag;
+ 
++void
+ merge_qds(db, t_f)
+      Database *db;
+      int t_f;
+@@ -1463,6 +1475,7 @@
+   }
+ }
+ 
++void
+ init_qd_trims(query_domain)
+      Query_domain *query_domain;
+ {
+@@ -1476,6 +1489,7 @@
+   init_qd_trims(query_domain->child[1]);
+ }
+ 
++void
+ test_qd1_merges(query_domain1, query_domain2)
+      Query_domain *query_domain1, *query_domain2;
+ {
+@@ -1486,6 +1500,7 @@
+   test_qd1_merges(query_domain1->child[1], query_domain2);
+ }
+ 
++void
+ test_qd2_merges(query_domain1, query_domain2)
+      Query_domain *query_domain1, *query_domain2;
+ {
+@@ -1533,6 +1548,7 @@
+   }
+ }
+ 
++void
+ compare_query_domains(query_domain1, query_domain2)
+   Query_domain *query_domain1, *query_domain2;
+ {
+@@ -1570,6 +1586,7 @@
+   }
+ }
+ 
++void
+ print_score_list(entry, query_domain)
+      int entry;
+      Query_domain *query_domain;
+@@ -1732,6 +1749,7 @@
+   }
+ }
+ 
++void
+ print_pair(pair, fp, no_zero)
+      Aligned_pair *pair;
+      FILE *fp;
+@@ -4125,6 +4143,7 @@
+   notify("done");
+ }
+ 
++void
+ revise_qd_scores(query_domain)
+      Query_domain *query_domain;
+ {