1 files changed, 64 insertions, 0 deletions
diff --git a/biology/phrap/files/patch-words.c b/biology/phrap/files/patch-words.c
new file mode 100644
index 000000000000..ed36f2bee041
--- /dev/null
+++ b/biology/phrap/files/patch-words.c
@@ -0,0 +1,64 @@
+--- ./words.c.orig	2009-04-22 20:48:22.000000000 +0200
++++ ./words.c	2014-08-02 12:39:30.000000000 +0200
+@@ -59,6 +59,12 @@
+ static unsigned char *long_word_array;
+ static int n_skips[3];
+ 
++void print_word_counts();
++void set_lower_upper();
++void set_index_words(int,int,int);
++void find_external_word_matches(int, unsigned char *);
++void quicksort(SEQ_AREA, SEQ_AREA, int, int, SEQ_AREA *);
++void new_lookup_words(unsigned char *, int, SEQ_AREA, SEQ_AREA, int, int);
+ 
+ typedef struct sw_edge {
+   int curr0, curr1, curr2;
+@@ -323,6 +329,7 @@
+ 
+ /* only used when DNA_flag == 2 */
+ 
++void
+ set_lower_upper()
+ {
+   unsigned int word_int, word_reduced, last_word_reduced;
+@@ -540,6 +547,7 @@
+ /*
+  other input: total_length, num_entries, complexity_flag, alphabet_size, residues, minmatch, nlogn_diff, mod_value, index_shift */
+ 
++void
+ set_index_words(pass, trans_type, index_type)
+      int pass, trans_type, index_type;
+ {
+@@ -1070,7 +1078,7 @@
+    refinement in Sedgwick, but using bookkeeping of matching leading parts 
+    of words in a block to substantially improve
+    efficiency) */
+-
++void
+ quicksort(left, right, k_start, maxcheck, seq_offsets)
+      SEQ_AREA left, right;
+      int k_start, maxcheck;
+@@ -1532,6 +1540,7 @@
+ 
+ */ 
+  
++void
+ find_external_word_matches(e1, seq) 
+      int e1;
+      unsigned char *seq;
+@@ -1776,6 +1785,7 @@
+ int known_match_size, target_match_size, offset1, sub_check, reuse;
+ extern int num_pairs;
+ 
++void
+ new_lookup_words(seq1, trans_type, sa_l_lower, sa_u_upper, ss_displace, n_lc)
+      int trans_type, ss_displace, n_lc;
+      SEQ_AREA sa_l_lower, sa_u_upper;
+@@ -2850,6 +2860,7 @@
+   for (i = 0; i < 5; i++) num_merge_words[i] = 0;
+ }
+ 
++void
+ print_word_counts()
+ {
+   int i;