Package list tigr-glimmer / 5ac85bc
Refreshed patches Andreas Tille 7 years ago
3 changed file(s) with 43 addition(s) and 39 deletion(s). Raw diff Collapse all Expand all
0 Author: Steffen Moeller <moeller@pzr.uni-rostock.de>
1 LastChanged: Thu, 16 Oct 2003 17:33:46 +0200
2 Description: Provide main Makefile
3
04 --- /dev/null
1 +++ glimmer3.02/Makefile
5 +++ b/Makefile
26 @@ -0,0 +1,7 @@
37 +all:
48 + cd src; make
00 Author: Kumar Appaiah
11 Description: Fix #461691
22
3 --- glimmer3.02.orig/src/Common/delcher.cc
4 +++ glimmer3.02/src/Common/delcher.cc
3 --- a/src/Common/delcher.cc
4 +++ b/src/Common/delcher.cc
55 @@ -9,6 +9,7 @@
66
77 #include "delcher.hh"
1010
1111 const int COMMATIZE_BUFF_LEN = 50;
1212 // Length of buffer for creating string with commas
13 --- glimmer3.02.orig/src/Common/fasta.cc
14 +++ glimmer3.02/src/Common/fasta.cc
13 --- a/src/Common/fasta.cc
14 +++ b/src/Common/fasta.cc
1515 @@ -9,7 +9,7 @@
1616
1717 #include "fasta.hh"
2121
2222 void Fasta_Print
2323 (FILE * fp, const char * s, const char * hdr, int fasta_width)
24 --- glimmer3.02.orig/src/Common/gene.cc
25 +++ glimmer3.02/src/Common/gene.cc
24 --- a/src/Common/gene.cc
25 +++ b/src/Common/gene.cc
2626 @@ -10,6 +10,7 @@
2727 #include "delcher.hh"
2828 #include "gene.hh"
3131
3232 static const char COMPLEMENT_TABLE []
3333 = "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"
34 --- glimmer3.02.orig/src/Glimmer/anomaly.cc
35 +++ glimmer3.02/src/Glimmer/anomaly.cc
34 --- a/src/Glimmer/anomaly.cc
35 +++ b/src/Glimmer/anomaly.cc
3636 @@ -12,6 +12,7 @@
3737
3838 #include "anomaly.hh"
4141
4242 // Global variables
4343
44 --- glimmer3.02.orig/src/ICM/icm.cc
45 +++ glimmer3.02/src/ICM/icm.cc
44 --- a/src/ICM/icm.cc
45 +++ b/src/ICM/icm.cc
4646 @@ -15,6 +15,8 @@
4747
4848 #include "icm.hh"
5252 using namespace std;
5353
5454 extern int Verbose;
55 --- glimmer3.02.orig/src/Util/entropy-score.cc
56 +++ glimmer3.02/src/Util/entropy-score.cc
55 --- a/src/Util/entropy-score.cc
56 +++ b/src/Util/entropy-score.cc
5757 @@ -9,7 +9,7 @@
5858 // regions in it by entropy distance. Results are output
5959 // to stdout .
6363
6464 #include "entropy-score.hh"
6565
66 --- glimmer3.02.orig/src/Glimmer/glimmer3.cc
67 +++ glimmer3.02/src/Glimmer/glimmer3.cc
66 --- a/src/Glimmer/glimmer3.cc
67 +++ b/src/Glimmer/glimmer3.cc
6868 @@ -12,11 +12,10 @@
6969 // Copyright (c) 2006 University of Maryland Center for Bioinformatics
7070 // & Computational Biology
7878 static int For_Edwin = 0;
7979
8080
81 --- glimmer3.02.orig/src/ICM/build-icm.cc
82 +++ glimmer3.02/src/ICM/build-icm.cc
81 --- a/src/ICM/build-icm.cc
82 +++ b/src/ICM/build-icm.cc
8383 @@ -13,6 +13,7 @@
8484
8585 #include "build-icm.hh"
8888
8989 static int Genbank_Xlate_Code = 0;
9090 // Holds the Genbank translation table number that determines
91 --- glimmer3.02.orig/src/Util/extract.cc
92 +++ glimmer3.02/src/Util/extract.cc
91 --- a/src/Util/extract.cc
92 +++ b/src/Util/extract.cc
9393 @@ -9,7 +9,7 @@
9494 // sequences specified by coordinates. The resulting sequences
9595 // are output (in multifasta or two-string format) to stdout.
9999
100100 #include "extract.hh"
101101
102 --- glimmer3.02.orig/src/Glimmer/glimmer2.cc
103 +++ glimmer3.02/src/Glimmer/glimmer2.cc
102 --- a/src/Glimmer/glimmer2.cc
103 +++ b/src/Glimmer/glimmer2.cc
104104 @@ -37,6 +37,7 @@
105105 #include "delcher.h"
106106 #include "gene.h"
109109
110110 const int DEFAULT_MIN_GENE_LEN = 90;
111111 const double DEFAULT_MIN_OLAP_PERCENT = 0.10;
112 --- glimmer3.02.orig/src/Glimmer/long-orfs.cc
113 +++ glimmer3.02/src/Glimmer/long-orfs.cc
112 --- a/src/Glimmer/long-orfs.cc
113 +++ b/src/Glimmer/long-orfs.cc
114114 @@ -15,7 +15,7 @@
115115
116116 #include "long-orfs.hh"
120120
121121 // External variables
122122
123 --- glimmer3.02.orig/src/ICM/build-fixed.cc
124 +++ glimmer3.02/src/ICM/build-fixed.cc
123 --- a/src/ICM/build-fixed.cc
124 +++ b/src/ICM/build-fixed.cc
125125 @@ -12,6 +12,7 @@
126126
127127 #include "build-fixed.hh"
130130
131131 static FILE * Index_File_fp = NULL;
132132 // File containing a list of subscripts of strings to train model
133 --- glimmer3.02.orig/src/ICM/score-fixed.cc
134 +++ glimmer3.02/src/ICM/score-fixed.cc
133 --- a/src/ICM/score-fixed.cc
134 +++ b/src/ICM/score-fixed.cc
135135 @@ -8,6 +8,7 @@
136136
137137 #include "score-fixed.hh"
140140
141141 static char * Pos_Model_Path;
142142 // Name of file containing the positive model
143 --- glimmer3.02.orig/src/Util/multi-extract.cc
144 +++ glimmer3.02/src/Util/multi-extract.cc
143 --- a/src/Util/multi-extract.cc
144 +++ b/src/Util/multi-extract.cc
145145 @@ -10,7 +10,7 @@
146146 // resulting sequences are output (in multifasta or two-string format)
147147 // to stdout.
151151
152152 #include "multi-extract.hh"
153153
154 --- glimmer3.02.orig/src/Util/start-codon-distrib.cc
155 +++ glimmer3.02/src/Util/start-codon-distrib.cc
154 --- a/src/Util/start-codon-distrib.cc
155 +++ b/src/Util/start-codon-distrib.cc
156156 @@ -17,6 +17,7 @@
157157
158158 #include "start-codon-distrib.hh"
161161
162162 // External variables
163163
164 --- glimmer3.02.orig/src/Util/uncovered.cc
165 +++ glimmer3.02/src/Util/uncovered.cc
164 --- a/src/Util/uncovered.cc
165 +++ b/src/Util/uncovered.cc
166166 @@ -10,7 +10,7 @@
167167 // specified in the file named as the second command-line argument.
168168 // Output is a multifasta file sent to stdout.
00 Author: Andreas Tille <tille@debian.org>
11 Description: Fix FTBFS #560442
22
3 --- tigr-glimmer-3.02.orig/src/Common/gene.cc
4 +++ tigr-glimmer-3.02/src/Common/gene.cc
5 @@ -444,7 +444,7 @@
3 --- a/src/Common/gene.cc
4 +++ b/src/Common/gene.cc
5 @@ -444,7 +444,7 @@ int Char_Sub
66 // Return a subscript corresponding to character ch .
77
88 {
1111
1212 p = strchr (CONVERSION_STRING, tolower (ch));
1313 if (p == NULL)
14 --- tigr-glimmer-3.02.orig/src/ICM/icm.cc
15 +++ tigr-glimmer-3.02/src/ICM/icm.cc
16 @@ -1983,7 +1983,7 @@
14 --- a/src/ICM/icm.cc
15 +++ b/src/ICM/icm.cc
16 @@ -1983,7 +1983,7 @@ int Subscript
1717 // model) for character ch .
1818
1919 {