Package list tigr-glimmer / a77e21a
gcc-4.3 patches Andreas Tille 14 years ago
3 changed file(s) with 174 addition(s) and 0 deletion(s). Raw diff Collapse all Expand all
0 --- glimmer3.02.orig/src/Common/delcher.cc
1 +++ glimmer3.02/src/Common/delcher.cc
2 @@ -9,6 +9,7 @@
3
4 #include "delcher.hh"
5
6 +#include <cstring>
7
8 const int COMMATIZE_BUFF_LEN = 50;
9 // Length of buffer for creating string with commas
10 --- glimmer3.02.orig/src/Common/fasta.cc
11 +++ glimmer3.02/src/Common/fasta.cc
12 @@ -9,7 +9,7 @@
13
14 #include "fasta.hh"
15
16 -
17 +#include <cstring>
18
19 void Fasta_Print
20 (FILE * fp, const char * s, const char * hdr, int fasta_width)
21 --- glimmer3.02.orig/src/Common/gene.cc
22 +++ glimmer3.02/src/Common/gene.cc
23 @@ -10,6 +10,7 @@
24 #include "delcher.hh"
25 #include "gene.hh"
26
27 +#include <cstring>
28
29 static const char COMPLEMENT_TABLE []
30 = "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"
31 --- glimmer3.02.orig/src/Glimmer/anomaly.cc
32 +++ glimmer3.02/src/Glimmer/anomaly.cc
33 @@ -12,6 +12,7 @@
34
35 #include "anomaly.hh"
36
37 +#include <cstring>
38
39 // Global variables
40
41 --- glimmer3.02.orig/src/ICM/icm.cc
42 +++ glimmer3.02/src/ICM/icm.cc
43 @@ -15,6 +15,8 @@
44
45 #include "icm.hh"
46
47 +#include <cstring>
48 +
49 using namespace std;
50
51 extern int Verbose;
52 --- glimmer3.02.orig/src/Util/entropy-score.cc
53 +++ glimmer3.02/src/Util/entropy-score.cc
54 @@ -9,7 +9,7 @@
55 // regions in it by entropy distance. Results are output
56 // to stdout .
57
58 -
59 +#include <cstring>
60
61 #include "entropy-score.hh"
62
63 --- glimmer3.02.orig/src/Glimmer/glimmer3.cc
64 +++ glimmer3.02/src/Glimmer/glimmer3.cc
65 @@ -12,11 +12,10 @@
66 // Copyright (c) 2006 University of Maryland Center for Bioinformatics
67 // & Computational Biology
68
69 -
70 +#include <cstring>
71
72 #include "glimmer3.hh"
73
74 -
75 static int For_Edwin = 0;
76
77
78 --- glimmer3.02.orig/src/ICM/build-icm.cc
79 +++ glimmer3.02/src/ICM/build-icm.cc
80 @@ -13,6 +13,7 @@
81
82 #include "build-icm.hh"
83
84 +#include <cstring>
85
86 static int Genbank_Xlate_Code = 0;
87 // Holds the Genbank translation table number that determines
88 --- glimmer3.02.orig/src/Util/extract.cc
89 +++ glimmer3.02/src/Util/extract.cc
90 @@ -9,7 +9,7 @@
91 // sequences specified by coordinates. The resulting sequences
92 // are output (in multifasta or two-string format) to stdout.
93
94 -
95 +#include <cstring>
96
97 #include "extract.hh"
98
99 --- glimmer3.02.orig/src/Glimmer/glimmer2.cc
100 +++ glimmer3.02/src/Glimmer/glimmer2.cc
101 @@ -37,6 +37,7 @@
102 #include "delcher.h"
103 #include "gene.h"
104
105 +#include <cstring>
106
107 const int DEFAULT_MIN_GENE_LEN = 90;
108 const double DEFAULT_MIN_OLAP_PERCENT = 0.10;
109 --- glimmer3.02.orig/src/Glimmer/long-orfs.cc
110 +++ glimmer3.02/src/Glimmer/long-orfs.cc
111 @@ -15,7 +15,7 @@
112
113 #include "long-orfs.hh"
114
115 -
116 +#include <cstring>
117
118 // External variables
119
120 --- glimmer3.02.orig/src/ICM/build-fixed.cc
121 +++ glimmer3.02/src/ICM/build-fixed.cc
122 @@ -12,6 +12,7 @@
123
124 #include "build-fixed.hh"
125
126 +#include <cstring>
127
128 static FILE * Index_File_fp = NULL;
129 // File containing a list of subscripts of strings to train model
130 --- glimmer3.02.orig/src/ICM/score-fixed.cc
131 +++ glimmer3.02/src/ICM/score-fixed.cc
132 @@ -8,6 +8,7 @@
133
134 #include "score-fixed.hh"
135
136 +#include <cstring>
137
138 static char * Pos_Model_Path;
139 // Name of file containing the positive model
140 --- glimmer3.02.orig/src/Util/multi-extract.cc
141 +++ glimmer3.02/src/Util/multi-extract.cc
142 @@ -10,7 +10,7 @@
143 // resulting sequences are output (in multifasta or two-string format)
144 // to stdout.
145
146 -
147 +#include <cstring>
148
149 #include "multi-extract.hh"
150
151 --- glimmer3.02.orig/src/Util/start-codon-distrib.cc
152 +++ glimmer3.02/src/Util/start-codon-distrib.cc
153 @@ -17,6 +17,7 @@
154
155 #include "start-codon-distrib.hh"
156
157 +#include <cstring>
158
159 // External variables
160
161 --- glimmer3.02.orig/src/Util/uncovered.cc
162 +++ glimmer3.02/src/Util/uncovered.cc
163 @@ -10,7 +10,7 @@
164 // specified in the file named as the second command-line argument.
165 // Output is a multifasta file sent to stdout.
166
167 -
168 +#include <cstring>
169
170 #include "uncovered.hh"
171
00 01_Makefile.patch
1 10_gcc4.3.patch
1919
2020 clean::
2121 dh_clean $(MANPAGES)
22 cd src; make clean
2223 rm -f bin/* lib/* obj/*
2324
2425 build/tigr-glimmer:: $(MANPAGES)