update ports:

	biology/phrab
	biology/phred
	biology/consed

Although these programs are licensed freely for academic and nonprofit
purposes, users have to contact the authors to obtain the tarballs.

PR:		191336
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)

18 files changed, 566 insertions, 18 deletions

diff --git a/biology/phrap/files/patch-alignments.c b/biology/phrap/files/patch-alignments.c
new file mode 100644
index 000000000000..986799024563
--- /dev/null
+++ b/biology/phrap/files/patch-alignments.c
@@ -0,0 +1,10 @@
+--- ./alignments.c.orig	2009-04-18 23:07:41.000000000 +0200
++++ ./alignments.c	2014-08-02 12:39:30.000000000 +0200
+@@ -591,6 +591,7 @@
+   return adj_score;
+ }
+ 
++void
+ print_alignment(profile)
+      Profile *profile;
+ {
diff --git a/biology/phrap/files/patch-analyze_splices.c b/biology/phrap/files/patch-analyze_splices.c
new file mode 100644
index 000000000000..bb3f5fe42475
--- /dev/null
+++ b/biology/phrap/files/patch-analyze_splices.c
@@ -0,0 +1,88 @@
+--- ./analyze_splices.c.orig	2008-08-31 03:37:44.000000000 +0200
++++ ./analyze_splices.c	2014-08-02 12:39:30.000000000 +0200
+@@ -146,6 +146,13 @@
+ char *exon_seq;
+ double base_llr, intron_coeff;
+ 
++void find_left_sites(Aligned_pair *, Cand_pair *, char *, char *);
++void find_right_sites(Aligned_pair *, Cand_pair *, char *, char *);
++void increment_splice_site(unsigned char *, unsigned char *,
++	Aligned_pair *, int, int, int, unsigned char *, int);
++void scan(Splice_site *, Aligned_pair *, unsigned char *,
++	int, int, int, int);
++
+ set_splice_params()
+ {
+   int i, j;
+@@ -186,6 +193,7 @@
+    cases of large missing exons: want to make sure this part of read doesn't match somewhere else, instead
+ */
+ 
++void
+ append_cand_splice(strand, left_splice_site, right_splice_site, overlap, intron_length, left_pair, right_pair)
+      int strand, overlap, intron_length;
+      Splice_site *left_splice_site, *right_splice_site;
+@@ -512,6 +520,7 @@
+   return penalty;
+ }
+ 
++void
+ check_best_site(pair, side, cand_pair)
+   Aligned_pair *pair;
+   int side;
+@@ -560,6 +569,7 @@
+ 
+ int extend[3];
+ 
++void
+ find_left_sites(pair, cand_pair, seq1, seq2)
+   Aligned_pair *pair;
+   Cand_pair *cand_pair;
+@@ -651,6 +661,7 @@
+ 
+ }
+ 
++void
+ find_right_sites(pair, cand_pair, seq1, seq2)
+   Aligned_pair *pair;
+   Cand_pair *cand_pair;
+@@ -816,6 +827,7 @@
+ This doesn't really address multiple testing issue; 
+ */
+ 
++void
+ increment_splice_site(seq1, seq2, pair, strand, side, loc, seq, type)
+      Aligned_pair *pair;
+      int strand, side, loc, type;
+@@ -922,6 +934,7 @@
+ 
+ /* input: splice_site, c_len, pair, seq1, exon_seq, genome_overhang, cdna_overhang, base_llr, intron_coeff, max_i  */
+ 
++void
+ scan(splice_site, pair, seq1, genome_overhang, cdna_overhang, max_i, test_len)
+   Splice_site *splice_site;
+   Aligned_pair *pair;
+@@ -1098,6 +1111,7 @@
+   return n_matches;
+ }
+ 
++void
+ check_max_length(length)
+      int length;
+ {
+@@ -1118,6 +1132,7 @@
+   max_length = length;
+ }
+ 
++void
+ filter_matches(i_ptr, n_p, pair_pointers, print_flag)
+      int i_ptr, n_p, print_flag;
+      Aligned_pair **pair_pointers;
+@@ -1276,6 +1291,7 @@
+   return seg_equiv1->start - seg_equiv2->start;
+ }
+ 
++void
+ analyze_multiple(i_ptr, n_p, pair_pointers, print_flag)
+      int i_ptr, n_p, print_flag;
+      Aligned_pair **pair_pointers;
diff --git a/biology/phrap/files/patch-anomalies.c b/biology/phrap/files/patch-anomalies.c
new file mode 100644
index 000000000000..508d4cd9de69
--- /dev/null
+++ b/biology/phrap/files/patch-anomalies.c
@@ -0,0 +1,19 @@
+--- ./anomalies.c.orig	2008-11-10 06:02:00.000000000 +0100
++++ ./anomalies.c	2014-08-02 12:39:30.000000000 +0200
+@@ -28,6 +28,8 @@
+ extern Parameters *parameters;
+ extern int num_pairs, t_num_entries;
+ 
++void visit_cand_pairs_dups(int, Cand_pair *);
++
+ #define MAX_CHIMERA_GAP 30  /* maximum gap between distinct confirmed segments for 
+ 			       putative chimeras */
+ compare_pair_entries(pair_1, pair_2)
+@@ -830,6 +832,7 @@
+   notify(" Done\n");
+ }
+ 
++void
+ visit_cand_pairs_dups(entry1, pair)
+      int entry1;
+      Cand_pair *pair;
diff --git a/biology/phrap/files/patch-calf_utils.c b/biology/phrap/files/patch-calf_utils.c
new file mode 100644
index 000000000000..9a09fb4d1c49
--- /dev/null
+++ b/biology/phrap/files/patch-calf_utils.c
@@ -0,0 +1,19 @@
+--- ./calf_utils.c.orig	2008-11-04 23:21:50.000000000 +0100
++++ ./calf_utils.c	2014-08-02 12:39:30.000000000 +0200
+@@ -28,6 +28,8 @@
+ 
+ extern void *malloc(), *realloc();
+ 
++void read_type_3(File_stat *, int);
++
+ append_file_stat(file_name)
+      char *file_name;
+ {
+@@ -110,6 +112,7 @@
+   get_record_header(file_stat);
+ }
+ 
++void
+ read_type_3(file_stat, new_rec_flag)
+      File_stat *file_stat;
+      int new_rec_flag;
diff --git a/biology/phrap/files/patch-call_subs.c b/biology/phrap/files/patch-call_subs.c
new file mode 100644
index 000000000000..8ee1379afc28
--- /dev/null
+++ b/biology/phrap/files/patch-call_subs.c
@@ -0,0 +1,19 @@
+--- ./call_subs.c.orig	1999-01-17 00:42:56.000000000 +0100
++++ ./call_subs.c	2014-08-02 12:39:30.000000000 +0200
+@@ -26,15 +26,13 @@
+ 
+ extern Parameters *parameters; 
+ 
++void
+ call_write_exp_files(n_sing, n_contigs, contig_ptrs)
+      int n_sing, n_contigs;
+      Contig **contig_ptrs;
+ {
+ #if defined(GCPHRAP)
+   write_exp_files(n_sing, n_contigs, contig_ptrs);
+-  return;
+-#else
+-  return;
+ #endif
+ }
+ 
diff --git a/biology/phrap/files/patch-cand_pairs.c b/biology/phrap/files/patch-cand_pairs.c
new file mode 100644
index 000000000000..6765364b7544
--- /dev/null
+++ b/biology/phrap/files/patch-cand_pairs.c
@@ -0,0 +1,18 @@
+--- ./cand_pairs.c.orig	2008-08-31 03:02:56.000000000 +0200
++++ ./cand_pairs.c	2014-08-02 12:39:30.000000000 +0200
+@@ -38,6 +38,7 @@
+ 
+ static int num_cand_pairs, num_dups, num_repeat_rejected_pairs;
+ 
++void
+ cluster_pairs(entry1, entry2, start1, start2, reverse, rev_store_flag)
+      int entry1, entry2, start1, start2;
+      int reverse, rev_store_flag;
+@@ -74,6 +75,7 @@
+   set_equiv_class(entry, final_class);
+ }
+ 
++void
+ make_new_cand_pair(entry1, entry2, start1, start2, reverse, rev_store_flag)
+      int entry1, entry2, start1, start2;
+      int reverse, rev_store_flag;
diff --git a/biology/phrap/files/patch-contigs.c b/biology/phrap/files/patch-contigs.c
new file mode 100644
index 000000000000..a2f99c774dc9
--- /dev/null
+++ b/biology/phrap/files/patch-contigs.c
@@ -0,0 +1,10 @@
+--- ./contigs.c.orig	2008-11-11 22:56:27.000000000 +0100
++++ ./contigs.c	2014-08-02 12:39:30.000000000 +0200
+@@ -2115,6 +2115,7 @@
+    contig1->base_segment = previous_base_segment;
+ }
+ 
++void
+ write_contigs()
+ {
+   char *our_alloc();
diff --git a/biology/phrap/files/patch-db.c b/biology/phrap/files/patch-db.c
new file mode 100644
index 000000000000..ae100313b440
--- /dev/null
+++ b/biology/phrap/files/patch-db.c
@@ -0,0 +1,19 @@
+--- ./db.c.orig	2009-04-21 18:10:09.000000000 +0200
++++ ./db.c	2014-08-02 12:39:30.000000000 +0200
+@@ -38,6 +38,8 @@
+ int qseq_trans[256];
+ int t_num_entries;
+ 
++void size_conflict(SEQ_AREA,long int,char *);
++
+ typedef long int POS;
+ static POS id_pos, descrip_pos, seq_pos, seq_length;
+ /* N.B. following needed by Bonfield code, so original "static" designation has
+@@ -571,6 +573,7 @@
+ 	 (unsigned long int)db->seq_area_size, (unsigned long int)db->id_area_size, (unsigned long int)db->descrip_area_size);
+ }
+ 
++void
+ size_conflict(size1, size2, label)
+      SEQ_AREA size1;
+      long int size2;
diff --git a/biology/phrap/files/patch-makefile b/biology/phrap/files/patch-makefile
index 7fccdb3846a1..2a83cd9e1e44 100644
--- a/biology/phrap/files/patch-makefile
+++ b/biology/phrap/files/patch-makefile
@@ -1,9 +1,9 @@
---- makefile.orig	1999-03-11 15:13:20.000000000 +0900
-+++ makefile	2007-12-11 13:19:39.000000000 +0900
-@@ -23,8 +23,8 @@
- #*****************************************************************************/
- 
+--- ./makefile.orig	2009-06-02 17:45:34.000000000 +0200
++++ ./makefile	2014-08-02 12:43:45.000000000 +0200
+@@ -25,8 +25,8 @@
  # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated)
+ #CC= icc
+ #CFLAGS= -O2 -wd266,880
 -CC= cc
 -CFLAGS= -O2
 +CC?= cc
@@ -11,17 +11,24 @@
  LFLAGS= -lm
  
  SWATOBJS= swat.o weibull.o
-@@ -55,11 +55,11 @@
+@@ -55,7 +55,7 @@
+ 
+ CALFOBJS= calf_merge.o  calf_utils.o
+ 
+-all:  swat phrap cross_match phrapview cluster loco calf_merge
++all:  swat phrap cross_match phrapview pcluster loco calf_merge
+ 
+ #manyreads:  
+ #	touch swat.h;
+@@ -131,9 +131,9 @@
+ 	$(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS)
+ 	chmod o-r gccross_match
+ 
+-cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS)
++pcluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS)
+ 	$(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS)
+-	chmod o-r cluster
++	chmod o-r pcluster
  
- manyreads:  
- 	touch swat.h;
--	make CFLAGS="-O2 -DMANYREADS" phrap cross_match;
-+	make CFLAGS="$(CFLAGS) -DMANYREADS" phrap cross_match;
- 	mv phrap phrap.manyreads;
- 	mv cross_match cross_match.manyreads;
- 	touch swat.h;
--	make CFLAGS="-O2 -DLONGREADS" phrap;
-+	make CFLAGS="$(CFLAGS) -DLONGREADS" phrap;
- 	mv phrap phrap.longreads;
- 	touch swat.h;
- 	make phrap cross_match;
+ loco: makefile $(LOCOOBJS) $(SWOBJS)
+ 	$(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS)
diff --git a/biology/phrap/files/patch-names.c b/biology/phrap/files/patch-names.c
new file mode 100644
index 000000000000..4b6ef3dd9526
--- /dev/null
+++ b/biology/phrap/files/patch-names.c
@@ -0,0 +1,19 @@
+--- ./names.c.orig	2007-11-06 23:03:53.000000000 +0100
++++ ./names.c	2014-08-02 12:39:30.000000000 +0200
+@@ -30,6 +30,8 @@
+ 
+ #define MAX_SUBCLONE_HIST 101
+ 
++void print_contig_chains();
++
+ set_delims()
+ {
+   subclone_delim = parameters->subclone_delim;
+@@ -1014,6 +1016,7 @@
+ 
+ /* greedy algorithm for finding chains of contigs */
+ /* NEED TO LOOK SYSTEMATICALLY FOR CIRCULAR CHAINS, AND BREAK THEM */
++void
+ print_contig_chains()
+ {
+   Link *link;
diff --git a/biology/phrap/files/patch-nodes.c b/biology/phrap/files/patch-nodes.c
new file mode 100644
index 000000000000..50af42003571
--- /dev/null
+++ b/biology/phrap/files/patch-nodes.c
@@ -0,0 +1,19 @@
+--- ./nodes.c.orig	2008-08-31 03:44:15.000000000 +0200
++++ ./nodes.c	2014-08-02 12:39:30.000000000 +0200
+@@ -31,6 +31,8 @@
+ extern Parameters *parameters; /* exported */
+ extern double *scaled_err_probs;
+ int *contig_graph_weights;
++
++void nr_tarjan(int);
+  
+ set_contig_graph_weights()
+ {
+@@ -679,6 +681,7 @@
+   curr_state->calling_point = calling_point;
+ }
+     
++void
+ nr_tarjan(k) 
+      int k;
+ {
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;
+ {
diff --git a/biology/phrap/files/patch-qual.c b/biology/phrap/files/patch-qual.c
new file mode 100644
index 000000000000..5c7627f1eb3a
--- /dev/null
+++ b/biology/phrap/files/patch-qual.c
@@ -0,0 +1,82 @@
+--- ./qual.c.orig	2008-11-12 17:45:48.000000000 +0100
++++ ./qual.c	2014-08-02 12:39:30.000000000 +0200
+@@ -44,6 +44,12 @@
+ static int mismatch_LLR[256];
+ double *scaled_err_probs; /* used for finding high-quality segments */
+ 
++void read_qual(Database *);
++void rescale_qual(Database *);
++void incr_diff_hist(unsigned char *, unsigned char *,
++	int, int, int, int, 
++	int, int, int, int );
++
+ init_qual_arrays()
+ {
+   int i;
+@@ -580,6 +586,7 @@
+ }
+ 
+ /* read in quality data */
++void
+ read_qual(db)
+      Database *db;
+ {
+@@ -876,6 +883,7 @@
+ }
+ 
+ /* NOT CORRECT WITH COMPRESSED QUAL */
++void
+ rescale_qual(db)
+      Database *db;
+ {
+@@ -1153,6 +1161,10 @@
+   int conf_count[2], conf_max_score, conf_max_margin; /* # confirming reads */
+ } Diffsegnode;
+ 
++void append_diffdata(Diffsegnode *);
++void append_diffsegnode(Diffsegnode *, int, int, int, int, Diffsegnode *);
++void write_diffsegnode(Diffsegnode *);
++
+ int data_type, data_length, data_qual, data_reverse, data_score, data_margin;
+ unsigned char *data_seq;
+ 
+@@ -1400,6 +1412,7 @@
+       = n_align[i] = n_unalign[i] = n_p_unalign[i] = 0;
+ }
+  
++void
+ incr_diff_hist(seq, diff, length1, length2, start1, start2, end1, end2, reverse, ignore_ends)
+      unsigned char *seq;
+      unsigned char *diff;
+@@ -1543,6 +1556,7 @@
+ int node_index;
+ extern unsigned char area_comp_mat[];
+ 
++void
+ append_diffdata(diffsegnode)
+      Diffsegnode *diffsegnode;
+ {
+@@ -1607,6 +1621,7 @@
+   diffdata->count[!data_reverse] = 0;
+ }
+ 
++void
+ append_diffsegnode(node, entry, seg_start, seg_end, conf_flag, data_node)
+      Diffsegnode *node, *data_node; /* latter is 0 if reading from global vars */
+      int entry, seg_start, seg_end, conf_flag;
+@@ -1724,6 +1739,7 @@
+   strcpy(cdb, "CDSILRdi");
+ }
+ 
++void
+ write_diffsegnode(node)
+      Diffsegnode *node;
+ {
+@@ -1800,6 +1816,7 @@
+   write_diffsegnode(node->child[1]);
+ }
+ 
++void
+ write_diffsegnodes()
+ {
+   int i;
diff --git a/biology/phrap/files/patch-readin.c b/biology/phrap/files/patch-readin.c
new file mode 100644
index 000000000000..0e30d7872bd6
--- /dev/null
+++ b/biology/phrap/files/patch-readin.c
@@ -0,0 +1,10 @@
+--- ./readin.c.orig	2008-11-11 20:33:41.000000000 +0100
++++ ./readin.c	2014-08-02 12:39:30.000000000 +0200
+@@ -31,6 +31,7 @@
+ /* read in sequence files, initialize array of aligned read info, and log file of ancillary information,
+  and find pairwise matches */
+ 
++void
+ readin_and_match()
+ {
+   File *file;
diff --git a/biology/phrap/files/patch-segments.c b/biology/phrap/files/patch-segments.c
new file mode 100644
index 000000000000..950899da7b15
--- /dev/null
+++ b/biology/phrap/files/patch-segments.c
@@ -0,0 +1,18 @@
+--- ./segments.c.orig	2008-07-30 19:14:13.000000000 +0200
++++ ./segments.c	2014-08-02 12:39:30.000000000 +0200
+@@ -112,6 +112,7 @@
+   return head;
+ }
+ 
++void
+ print_segments(head, index, complement) 
+      Segment *head;
+      int index;
+@@ -128,6 +129,7 @@
+   } 
+ }
+ 
++void
+ old_print_segments(head, index1, index2, offset, rel_orient) 
+      Segment *head;
+      int index1, index2, offset;
diff --git a/biology/phrap/files/patch-tig_node.c b/biology/phrap/files/patch-tig_node.c
new file mode 100644
index 000000000000..d2506b8beeda
--- /dev/null
+++ b/biology/phrap/files/patch-tig_node.c
@@ -0,0 +1,18 @@
+--- ./tig_node.c.orig	2007-11-06 23:02:49.000000000 +0100
++++ ./tig_node.c	2014-08-02 12:39:30.000000000 +0200
+@@ -138,6 +138,7 @@
+   tig_node->best_stack_length[0] = tig_node->best_stack_length[1] = 0;
+ }
+ 
++void
+ alloc_edge(contig, orientation, pair, reverse)
+      Contig *contig;
+      int orientation, reverse;
+@@ -176,6 +177,7 @@
+   tig_node->edges[orientation] = edge;
+ }
+ 
++void
+ find_best_paths(gap_cutoff, LLR_reject_cutoff, LLR_join_cutoff)
+      int gap_cutoff, LLR_reject_cutoff, LLR_join_cutoff;
+ {
diff --git a/biology/phrap/files/patch-weibull.c b/biology/phrap/files/patch-weibull.c
new file mode 100644
index 000000000000..1e8de65cb2b6
--- /dev/null
+++ b/biology/phrap/files/patch-weibull.c
@@ -0,0 +1,18 @@
+--- ./weibull.c.orig	2008-07-29 20:06:24.000000000 +0200
++++ ./weibull.c	2014-08-02 12:39:30.000000000 +0200
+@@ -77,6 +77,7 @@
+   z_cutoff = Z_CUTOFF;
+ }
+ 
++void
+ update_hist(score_entry, z_flag)
+      Score_entry *score_entry;
+      int z_flag;
+@@ -103,6 +104,7 @@
+   score2_sums[length] += score * score;
+ }  
+ 
++void
+ prune_hist(score_entry)
+      Score_entry *score_entry;
+ {
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;