Codebase list genometools / ee895fe
Remove unused patches Andreas Tille 5 years ago
12 changed file(s) with 0 addition(s) and 844 deletion(s). Raw diff Collapse all Expand all
+0
-16
debian/patches/add-libtre less more
0 Description: add soname to linker call in Makefile
1 Upstream Makefile does not build a shared object with soname or version
2 number. This patch adds support for sonames, as well a symlink from
3 the .so to the .so.X file.
4 Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
5 --- a/Makefile
6 +++ b/Makefile
7 @@ -191,7 +191,7 @@
8 # add necessary shared lib dependencies then not building them ourselves
9 ifeq ($(useshared),yes)
10 DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
11 - -llua5.1-filesystem -llua5.1-des56 -lbam
12 + -llua5.1-filesystem -llua5.1-des56 -lbam -ltre
13 else
14 DEPLIBS:=
15 endif
+0
-13
debian/patches/arm64-no-m64 less more
0 Description: Do not use -m64 in arm64.
1 Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
2 --- a/Makefile
3 +++ b/Makefile
4 @@ -308,7 +308,7 @@
5 endif
6
7 ifeq ($(m64),yes)
8 - ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el))
9 + ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el aarch64))
10 GT_CFLAGS += -m64
11 GT_LDFLAGS += -m64
12 SQLITE_CFLAGS += -m64
+0
-117
debian/patches/fix-unsigned-char less more
0 Description: Adapt code to work with char being unsigned by default.
1 Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
2 --- a/src/core/safearith.c
3 +++ b/src/core/safearith.c
4 @@ -182,8 +182,10 @@
5 gt_error_check(err);
6
7 {
8 + /* This is not always true, e.g. on PPC and ARM!
9 + cf. http://www.network-theory.co.uk/docs/gccintro/gccintro_71.html
10 gt_ensure(__MIN(char) == -128);
11 - gt_ensure(__MAX(char) == 127);
12 + gt_ensure(__MAX(char) == 127); */
13 gt_ensure(__MIN(unsigned char) == 0);
14 gt_ensure(__MAX(unsigned char) == 255);
15
16 --- a/src/core/tokenizer.c
17 +++ b/src/core/tokenizer.c
18 @@ -45,7 +45,9 @@
19
20 GtStr* gt_tokenizer_get_token(GtTokenizer *t)
21 {
22 - char c = EOF;
23 + char c;
24 + bool has_eof = true;
25 + int rval = 0;
26 gt_assert(t);
27
28 /* if we have no current token, get it if possible */
29 @@ -53,32 +55,44 @@
30 if (t->skip_comment_lines && gt_io_line_start(t->io)) {
31 for (;;) {
32 gt_assert(gt_io_line_start(t->io));
33 - if ((gt_io_get_char(t->io, &c) != -1)) {
34 - if (c == '#') {
35 + if ((gt_io_get_char(t->io, (char*) &c) != -1)) {
36 + if ((char) c == '#') {
37 /* skip line */
38 while ((gt_io_get_char(t->io, &c) != -1) && c != '\n');
39 - c = EOF;
40 + has_eof = true;
41 }
42 else {
43 gt_io_unget_char(t->io, c);
44 + has_eof = false;
45 break;
46 }
47 }
48 - else
49 + else {
50 + c = EOF;
51 break;
52 + }
53 }
54 - }
55 - while ((gt_io_get_char(t->io, &c) != -1) && c == ' '); /* skip blanks */
56 + } /* skip blanks */
57 + while (((rval = gt_io_get_char(t->io, &c)) != -1) && c == ' ');
58 + if (rval == -1)
59 + has_eof = true;
60 + else
61 + has_eof = false;
62 do {
63 - if (c != EOF) {
64 + if (!has_eof) {
65 if (!t->token)
66 t->token = gt_str_new();
67 if (c == '\n')
68 break;
69 gt_str_append_char(t->token, c);
70 }
71 - } while ((gt_io_get_char(t->io, &c) != -1) && c != ' ' && c != '\n');
72 - if (c == '\n' && c != EOF) {
73 + } while (((rval = gt_io_get_char(t->io, &c)) != -1)
74 + && c != ' ' && c != '\n');
75 + if (rval == -1)
76 + has_eof = true;
77 + else
78 + has_eof = false;
79 + if (c == '\n' && !has_eof) {
80 gt_assert(t->token);
81 gt_str_append_char(t->token, c);
82 }
83 --- a/src/core/tokenizer.h
84 +++ b/src/core/tokenizer.h
85 @@ -33,7 +33,7 @@
86 bool gt_tokenizer_has_token(GtTokenizer*);
87 bool gt_tokenizer_line_start(const GtTokenizer*);
88 void gt_tokenizer_next_token(GtTokenizer*); /* go to the next token */
89 -GtUword gt_tokenizer_get_line_number(const GtTokenizer*);
90 +GtUword gt_tokenizer_get_line_number(const GtTokenizer*);
91 const char* gt_tokenizer_get_filename(const GtTokenizer*);
92 int gt_tokenizer_unit_test(GtError*);
93 void gt_tokenizer_delete(GtTokenizer*);
94 --- a/src/core/trans_table.c
95 +++ b/src/core/trans_table.c
96 @@ -21,7 +21,7 @@
97 #include "core/ma.h"
98 #include "core/trans_table.h"
99
100 -#define GT_AMINOACIDFAIL -1
101 +#define GT_AMINOACIDFAIL ((char) 0)
102
103 /* The integer which a T is encoded to. */
104 #define GT_T_CODE 0
105 --- a/src/extended/gff3_escaping.c
106 +++ b/src/extended/gff3_escaping.c
107 @@ -64,7 +64,8 @@
108 unsigned char d;
109 gt_assert(str && out);
110 if (!(GtIsHexChar[(int) *(str+1)] & 2)
111 - || !(GtIsHexChar[(int) *(str+2)] & 1)) {
112 + || !(GtIsHexChar[(int) *(str+2)] & 1)
113 + || !strncmp(str, "%7F", 3 * (sizeof (char)))) {
114 return -1;
115 }
116 d = (GtHexToDec[(int) *(str+1)] << 4) | (GtHexToDec[(int) *(str+2)]);
+0
-13
debian/patches/fix_caption.patch less more
0 Description: change test caption to be less problematic
1 Author: Sascha Steinbiss <satta@debian.org>
2 Origin: https://github.com/genometools/genometools/commit/d86b83dda1eb43a5adf27f831b103f817e1dc48f#commitcomment-20423074
3 --- a/testdata/gt_sketch_textwidth.gff3
4 +++ b/testdata/gt_sketch_textwidth.gff3
5 @@ -1,6 +1,6 @@
6 ##gff-version 3
7 ##sequence-region ctg123 1 1497228
8 ctg123 . gene 1000 2000 . + 0 ID=g00001;Name=thisisalongname123
9 -ctg123 . gene 2001 3000 . + 0 ID=g00002;Name=anotherlongname123
10 +ctg123 . gene 2001 3000 . + 0 ID=g00002;Name=anotherlongname
11 ctg123 . gene 3001 4000 . + 0 ID=g00003;Name=stillanotherlonglonglonglonglonglonglongname
12 ctg123 . gene 4001 5000 . + 0 ID=g00004;Name=shortname
+0
-170
debian/patches/manual_fixed_dates.patch less more
0 From 3bf0e31b3a020c415d99d8661c5aca32647c7a6f Mon Sep 17 00:00:00 2001
1 From: Sascha Steinbiss <ss34@sanger.ac.uk>
2 Date: Thu, 7 Apr 2016 10:25:25 +0100
3 Subject: [PATCH] introduce dates for manuals
4
5 IMHO manuals should have a specific date, and the build date should not be
6 relevant here. This commit initialises the date fields in the manuals by
7 setting the date to the last modification date of the file in git, as
8 given by:
9
10 for f in doc/manuals/*.tex; do
11 export OUT=`TZ=UTC LC_ALL=C date -d "$(git log -1 --format='%aD' -- $f )" +'%d\/%m\/%Y'`;
12 sed -ri "s/.begin.document./\\\date{$OUT}\n\\\begin{document}/g" $f;
13 unset OUT;
14 done
15 ---
16 doc/manuals/annotationsketch.tex | 1 +
17 doc/manuals/genomediff.tex | 1 +
18 doc/manuals/hop.tex | 1 +
19 doc/manuals/ltrdigest.tex | 1 +
20 doc/manuals/ltrharvest.tex | 1 +
21 doc/manuals/mgth.tex | 1 +
22 doc/manuals/packedindex.tex | 1 +
23 doc/manuals/readjoiner.tex | 1 +
24 doc/manuals/repfind.tex | 1 +
25 doc/manuals/tagerator.tex | 1 +
26 doc/manuals/tallymer.tex | 1 +
27 doc/manuals/uniquesub.tex | 1 +
28 12 files changed, 12 insertions(+)
29
30 --- a/doc/manuals/annotationsketch.tex
31 +++ b/doc/manuals/annotationsketch.tex
32 @@ -50,6 +50,7 @@
33 \subject{Supplementary Information}
34 \author{Sascha Steinbiss, Gordon Gremme, Christin Sch\"arfer, Malte Mader\\ and Stefan Kurtz}
35
36 +\date{11/07/2012}
37 \begin{document}
38
39 \maketitle
40 --- a/doc/manuals/genomediff.tex
41 +++ b/doc/manuals/genomediff.tex
42 @@ -59,6 +59,7 @@
43 \url{willrodt@zbh.uni-hamburg.de}\\
44 \end{tabular}}
45
46 +\date{02/10/2012}
47 \begin{document}
48 %\tsuhhfamily
49 \maketitle
50 --- a/doc/manuals/hop.tex
51 +++ b/doc/manuals/hop.tex
52 @@ -32,6 +32,7 @@
53 \url{kurtz@zbh.uni-hamburg.de}\\[1cm]
54 \end{tabular}}
55
56 +\date{15/05/2014}
57 \begin{document}
58 \maketitle
59
60 --- a/doc/manuals/ltrdigest.tex
61 +++ b/doc/manuals/ltrdigest.tex
62 @@ -41,6 +41,7 @@
63 \end{tabular}
64 \end{tabular}}
65
66 +\date{26/08/2013}
67 \begin{document}
68 \maketitle
69
70 --- a/doc/manuals/ltrharvest.tex
71 +++ b/doc/manuals/ltrharvest.tex
72 @@ -41,6 +41,7 @@
73 \url{http://www.biomedcentral.com/1471-2105/9/18}
74 \end{tabular}
75 \end{tabular}}
76 +\date{26/08/2013}
77 \begin{document}
78 \maketitle
79
80 --- a/doc/manuals/mgth.tex
81 +++ b/doc/manuals/mgth.tex
82 @@ -37,6 +37,7 @@
83 20146 Hamburg\\
84 Germany\\[1cm]
85 \end{tabular}}
86 +\date{26/08/2013}
87 \begin{document}
88 \maketitle
89
90 --- a/doc/manuals/packedindex.tex
91 +++ b/doc/manuals/packedindex.tex
92 @@ -38,6 +38,7 @@
93 % BMC Bioinformatics 2008, 9:18
94 \end{tabular}
95 \end{tabular}}
96 +\date{26/08/2013}
97 \begin{document}
98 \maketitle
99
100 --- a/doc/manuals/readjoiner.tex
101 +++ b/doc/manuals/readjoiner.tex
102 @@ -45,6 +45,7 @@
103 \url{kurtz@zbh.uni-hamburg.de}\\[1cm]
104 \end{tabular}}
105
106 +\date{18/02/2014}
107 \begin{document}
108 \maketitle
109
110 --- a/doc/manuals/repfind.tex
111 +++ b/doc/manuals/repfind.tex
112 @@ -28,6 +28,7 @@
113 University of Hamburg
114 \end{tabular}}
115
116 +\date{26/08/2013}
117 \begin{document}
118 \maketitle
119 This manual describes the options of the program \Repfind. It also gives
120 --- a/doc/manuals/tagerator.tex
121 +++ b/doc/manuals/tagerator.tex
122 @@ -22,6 +22,7 @@
123 University of Hamburg
124 \end{tabular}}
125
126 +\date{26/08/2013}
127 \begin{document}
128 \maketitle
129
130 --- a/doc/manuals/tallymer.tex
131 +++ b/doc/manuals/tallymer.tex
132 @@ -95,6 +95,7 @@
133 University of Hamburg
134 \end{tabular}}
135
136 +\date{26/08/2013}
137 \begin{document}
138 \maketitle
139 This manual describes the \textit{Tallymer}-software, a collection of programs
140 --- a/doc/manuals/uniquesub.tex
141 +++ b/doc/manuals/uniquesub.tex
142 @@ -24,6 +24,7 @@
143 University of Hamburg
144 \end{tabular}}
145
146 +\date{26/08/2013}
147 \begin{document}
148 \maketitle
149
150 --- a/doc/devguide/devguide.tex
151 +++ b/doc/devguide/devguide.tex
152 @@ -36,6 +36,7 @@
153 \author{Sascha Steinbiss, Gordon Gremme and Stefan
154 Kurtz\thanks{please send comments to:
155 \texttt{steinbiss@zbh.uni-hamburg.de}}}
156 +\date{18/02/2016}
157
158
159 \begin{document}
160 --- a/doc/manuals/matstat.tex
161 +++ b/doc/manuals/matstat.tex
162 @@ -23,6 +23,7 @@
163 Center for Bioinformatics,\\
164 University of Hamburg
165 \end{tabular}}
166 +\date{26/01/2008}
167
168 \begin{document}
169 \maketitle
+0
-21
debian/patches/mips-64 less more
0 Description: Fix compilation on mips64.
1 Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
2 --- a/Makefile
3 +++ b/Makefile
4 @@ -308,12 +308,10 @@
5 endif
6
7 ifeq ($(m64),yes)
8 - ifneq ($(MACHINE),ia64)
9 - ifneq ($(MACHINE),alpha)
10 - GT_CFLAGS += -m64
11 - GT_LDFLAGS += -m64
12 - SQLITE_CFLAGS += -m64
13 - endif
14 + ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el))
15 + GT_CFLAGS += -m64
16 + GT_LDFLAGS += -m64
17 + SQLITE_CFLAGS += -m64
18 endif
19 endif
20
+0
-78
debian/patches/sort-inputs less more
0 Description: Sort inputs
1 --- a/Makefile
2 +++ b/Makefile
3 @@ -115,7 +115,7 @@
4 EXAMPLES_SRC:=src/example.c
5 EXAMPLES_DEP:=$(EXAMPLES_SRC:%.c=obj/%.d)
6
7 -TOOLS_SRC:=$(wildcard src/tools/*.c)
8 +TOOLS_SRC:=$(sort $(wildcard src/tools/*.c))
9 TOOLS_OBJ:=$(TOOLS_SRC:%.c=obj/%.o)
10 TOOLS_DEP:=$(TOOLS_SRC:%.c=obj/%.d)
11
12 @@ -449,7 +449,7 @@
13 endif
14
15 # the GenomeTools library
16 -LIBGENOMETOOLS_PRESRC:=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(wildcard $(DIR)/*.c))
17 +LIBGENOMETOOLS_PRESRC:=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(sort $(wildcard $(DIR)/*.c)))
18 # remove AnnotationSketch-only bindings
19 LIBGENOMETOOLS_PRESRC:=$(filter-out $(CAIRO_FILTER_OUT),\
20 $(LIBGENOMETOOLS_PRESRC))
21 @@ -664,7 +664,7 @@
22 @test -d $(@D) || mkdir -p $(@D)
23 @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $^ -lm $(LUA_LDLIB) -o $@
24
25 -API_HEADERS=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(wildcard $(DIR)/*_api.h))
26 +API_HEADERS=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(sort $(wildcard $(DIR)/*_api.h)))
27
28 obj/public_symbols.lst: $(API_HEADERS) $(LIBGENOMETOOLS_SRC)
29 @echo '[gathering public API symbols to $@]'
30 @@ -999,8 +999,8 @@
31 ABTOOLS=${shell grep -l Blaufelder src/tools/*.c}
32
33 ALLSPLINT=${addprefix obj/,${notdir ${subst .c,.splint,\
34 - ${filter-out ${EISFILES},${wildcard ${CURDIR}/src/match/*.c}}\
35 - ${wildcard ${CURDIR}/src/ltr/*.c}\
36 + ${filter-out ${EISFILES},${sort ${wildcard ${CURDIR}/src/match/*.c}}}\
37 + ${sort ${wildcard ${CURDIR}/src/ltr/*.c}}\
38 ${SKTOOLS} ${SKCORE} ${SKEXT} \
39 ${DWTOOLS} ${DWCORE} ${DWEXT} \
40 ${GGTOOLS} ${GGCORE} ${GGEXT} \
41 --- a/gtscripts/gtdoc.lua
42 +++ b/gtscripts/gtdoc.lua
43 @@ -104,6 +104,25 @@
44 end
45 end
46
47 +local function iter (a, i) -- taken from PiL, page 59
48 + i = i + 1
49 + local v = a[i]
50 + if v then
51 + return i, v
52 + end
53 +end
54 +
55 +function sorted_dir(dir)
56 + local entries = {}
57 + local i = 0
58 + for name in lfs.dir(dir) do
59 + i = i + 1
60 + entries[i] = name
61 + end
62 + table.sort(entries)
63 + return iter, entries, 0
64 +end
65 +
66 local export = nil
67 local is_lua = nil
68
69 @@ -127,7 +146,7 @@
70 for _, v in ipairs(export) do
71 local filename = gt_home .. "/" .. v
72 if is_dir(filename) then
73 - for f in lfs.dir(filename) do
74 + for _, f in sorted_dir(filename) do
75 local filename = filename .. "/" .. f
76 process_file(filename, be_verbose, is_lua)
77 end
+0
-5
debian/patches/spelling less more
0 Description: fix spelling issues
1 Author: Sascha Steinbiss <satta@debian.org>
2 Forwarded: https://github.com/genometools/genometools/pull/727, https://github.com/genometools/genometools/pull/762, https://github.com/genometools/genometools/pull/767
3 Applied-Upstream: 1.5.9, commit:f47cc4a6e13d037d6342b0213a5739031ada59c1
4 Last-Update: 2016-03-15
+0
-117
debian/patches/spelling.patch less more
0 Description: fix minor spelling issues
1 Author: Sascha Steinbiss <satta@debian.org>
2 --- a/src/extended/condenseq_creator.c
3 +++ b/src/extended/condenseq_creator.c
4 @@ -1723,7 +1723,7 @@
5 if (!had_err) {
6 if (gt_showtime_enabled())
7 gt_timer_show_progress(timer, "write data, alphabet", stderr);
8 - gt_log_log(GT_WU " kmer positons in final kmer_db",
9 + gt_log_log(GT_WU " kmer positions in final kmer_db",
10 gt_kmer_database_get_kmer_count(condenseq_creator->kmer_db));
11 gt_log_log(GT_WU " xdrop calls.", ces_c_xdrops);
12 gt_log_log(GT_WU " uniques", condenseq_creator->ces->udb_nelems);
13 --- a/src/extended/intset.h
14 +++ b/src/extended/intset.h
15 @@ -74,7 +74,7 @@
16 size_t gt_intset_best_memory_size(GtUword maxelement, GtUword num_of_elems);
17
18 /* Write <intset> to file <fp>. Fails with exit on IO-error. Returns NULL if
19 - data error occures and writes it to <err>, <intset> will be deleted at that
20 + data error occurs and writes it to <err>, <intset> will be deleted at that
21 point. */
22 GtIntset* gt_intset_write(GtIntset *intset, FILE *fp, GtError *err);
23
24 --- a/src/extended/wtree_encseq.c
25 +++ b/src/extended/wtree_encseq.c
26 @@ -84,7 +84,7 @@
27
28 if (bit == 0) {
29 pos = gt_compressed_bitsequence_rank_0(we->c_bits, node_start + pos) -
30 - zero_rank_prefix - 1; /*convert count (rank) to positon */
31 + zero_rank_prefix - 1; /*convert count (rank) to position */
32 alpha_end = middle;
33 node_start += we->parent_instance.members->length;
34 node_size = left_child_size;
35 @@ -96,7 +96,7 @@
36 one_rank_prefix =
37 gt_compressed_bitsequence_rank_1(we->c_bits, node_start - 1);
38 pos = gt_compressed_bitsequence_rank_1(we->c_bits, node_start + pos) -
39 - one_rank_prefix - 1; /*convert count (rank) to positon */
40 + one_rank_prefix - 1; /*convert count (rank) to position */
41 alpha_start = middle + 1;
42 node_size =
43 gt_compressed_bitsequence_rank_1(we->c_bits,
44 --- a/src/match/seqabstract.h
45 +++ b/src/match/seqabstract.h
46 @@ -71,7 +71,7 @@
47 /* return the length of <sa> */
48 GtUword gt_seqabstract_length(const GtSeqabstract *sa);
49
50 -/* return character at positon <idx> (relative to <startpos>) of <sa> */
51 +/* return character at position <idx> (relative to <startpos>) of <sa> */
52 GtUchar gt_seqabstract_encoded_char(const GtSeqabstract *sa,
53 GtUword idx);
54
55 --- a/src/match/sfx-diffcov.c
56 +++ b/src/match/sfx-diffcov.c
57 @@ -491,7 +491,7 @@
58 return countderived;
59 }
60
61 -static int dc_compareCodeatpositon(const void *vala,const void *valb)
62 +static int dc_compareCodeatposition(const void *vala,const void *valb)
63 {
64 const Codeatposition *a = (const Codeatposition *) vala;
65 const Codeatposition *b = (const Codeatposition *) valb;
66 @@ -516,7 +516,7 @@
67 return 0;
68 }
69
70 -static void dc_validate_samplepositons(const GtDifferencecover *dcov)
71 +static void dc_validate_samplepositions(const GtDifferencecover *dcov)
72 {
73 GtUword pos;
74 unsigned int modvalue;
75 @@ -1268,7 +1268,7 @@
76 gt_assert(codelist.spaceCodeatposition != NULL);
77 qsort(codelist.spaceCodeatposition,
78 (size_t) codelist.nextfreeCodeatposition,
79 - sizeof (*codelist.spaceCodeatposition),dc_compareCodeatpositon);
80 + sizeof (*codelist.spaceCodeatposition),dc_compareCodeatposition);
81 }
82 if (dcov->effectivesamplesize > 0)
83 {
84 @@ -1690,7 +1690,7 @@
85 printf("v=%u (size=%u)\n",dcov->vparam,dcov->size);
86 if (withcheck)
87 {
88 - dc_validate_samplepositons(dcov);
89 + dc_validate_samplepositions(dcov);
90 }
91 dc_differencecover_sortsample(dcov,NULL,NULL,NULL,withcheck);
92 gt_differencecover_delete(dcov);
93 --- a/src/tools/gt_kmer_database.c
94 +++ b/src/tools/gt_kmer_database.c
95 @@ -126,8 +126,8 @@
96 gt_option_exclude(option_mean_cutoff, option);
97
98 /* -disable_prune */
99 - option = gt_option_new_bool("disable_prune", "disables the removel of kmers, "
100 - "which occure more often than the cutoff.",
101 + option = gt_option_new_bool("disable_prune", "disables the removal of kmers "
102 + "which occur more often than the cutoff.",
103 &arguments->prune, false);
104 gt_option_parser_add_option(op, option);
105 gt_option_imply(option, option_use_cutoff);
106 --- a/src/tools/gt_show_seedext.c
107 +++ b/src/tools/gt_show_seedext.c
108 @@ -119,7 +119,7 @@
109
110 /* -sort */
111 op_sortmatches = gt_option_new_bool("sort","sort matches in ascending order "
112 - "of their end positon on the "
113 + "of their end position on the "
114 "query",
115 &arguments->sortmatches,false);
116 gt_option_parser_add_option(op, op_sortmatches);
+0
-17
debian/patches/strip-nonpublic less more
0 --- a/Makefile
1 +++ b/Makefile
2 @@ -894,8 +894,13 @@
3 $(RANLIB) $(prefix)/lib/libgenometools.a
4 endif
5 ifneq ($(sharedlib),no)
6 - cp lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) $(prefix)/lib
7 + find src -name '*_api.h' | xargs egrep -ho '(gt_[0-9a-zA-Z_]+)(\[|\()' \
8 + | sort | uniq | sed s'/.$$//' > apisyms
9 + objcopy --strip-all --keep-symbols apisyms \
10 + lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) \
11 + $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION)
12 ln -fs $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)
13 + rm apisyms
14 endif
15 @echo '[build config script $(@F)]'
16 sed -e 's!@CC@!$(CC)!' -e 's!@CFLAGS@!$(EXP_CFLAGS)!' \
+0
-224
debian/patches/typecheck-fixes less more
0 Description: Type conversion problem fixes.
1 Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
2 --- a/src/gtlua/encseq_lua.c
3 +++ b/src/gtlua/encseq_lua.c
4 @@ -80,8 +80,10 @@
5 GtReadmode readmode;
6 reader = check_encseq_reader(L, 1);
7 encseq = check_encseq(L, 2);
8 - readmode = luaL_checknumber(L, 3);
9 - startpos = luaL_checknumber(L, 4);
10 + readmode = luaL_checklong(L, 3);
11 + startpos = luaL_checklong(L, 4);
12 + luaL_argcheck(L, readmode <= 3, 3,
13 + "invalid readmode value, must be <= 3");
14 luaL_argcheck(L, startpos < gt_encseq_total_length(*encseq), 4,
15 "cannot exceed total length of encoded sequence");
16 gt_encseq_reader_reinit_with_readmode(*reader, *encseq, readmode, startpos);
17 @@ -113,10 +115,12 @@
18 int readmode;
19 unsigned char cc;
20 encseq = check_encseq(L, 1);
21 - pos = luaL_checknumber(L, 2);
22 - readmode = luaL_checknumber(L, 3);
23 + pos = luaL_checklong(L, 2);
24 + readmode = luaL_checklong(L, 3);
25 luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
26 "cannot exceed total length of encoded sequence");
27 + luaL_argcheck(L, readmode <= 3, 3,
28 + "invalid readmode value, must be <= 3");
29 cc = gt_encseq_get_encoded_char(*encseq, pos, readmode);
30 lua_pushnumber(L, cc);
31 return 1;
32 @@ -129,10 +133,12 @@
33 int readmode;
34 char cc;
35 encseq = check_encseq(L, 1);
36 - pos = luaL_checknumber(L, 2);
37 - readmode = luaL_checknumber(L, 3);
38 + pos = luaL_checklong(L, 2);
39 + readmode = luaL_checklong(L, 3);
40 luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
41 "cannot exceed total length of encoded sequence");
42 + luaL_argcheck(L, readmode <= 3, 3,
43 + "invalid readmode value, must be <= 3");
44 cc = gt_encseq_get_decoded_char(*encseq, pos, readmode);
45 lua_pushlstring(L, &cc, sizeof (char));
46 return 1;
47 @@ -192,8 +198,8 @@
48 GtUword from, to;
49 unsigned char *string;
50 encseq = check_encseq(L, 1);
51 - from = luaL_checknumber(L, 2);
52 - to = luaL_checknumber(L, 3);
53 + from = luaL_checklong(L, 2);
54 + to = luaL_checklong(L, 3);
55 luaL_argcheck(L, from <= to, 2, "must be <= range endposition");
56 luaL_argcheck(L, to < gt_encseq_total_length(*encseq), 3,
57 "cannot exceed total length of encoded sequence");
58 @@ -209,8 +215,8 @@
59 GtUword from, to;
60 char *string;
61 encseq = check_encseq(L, 1);
62 - from = luaL_checknumber(L, 2);
63 - to = luaL_checknumber(L, 3);
64 + from = luaL_checklong(L, 2);
65 + to = luaL_checklong(L, 3);
66 luaL_argcheck(L, from <= to, 2, "must be <= range endposition");
67 luaL_argcheck(L, to < gt_encseq_total_length(*encseq), 3,
68 "cannot exceed total length of encoded sequence");
69 @@ -226,7 +232,7 @@
70 GtEncseq **encseq;
71 GtUword pos;
72 encseq = check_encseq(L, 1);
73 - pos = luaL_checknumber(L, 2);
74 + pos = luaL_checklong(L, 2);
75 luaL_argcheck(L, pos < gt_encseq_num_of_sequences(*encseq), 2,
76 "cannot exceed number of sequences");
77 lua_pushnumber(L, gt_encseq_seqlength(*encseq, pos));
78 @@ -238,7 +244,7 @@
79 GtEncseq **encseq;
80 GtUword pos;
81 encseq = check_encseq(L, 1);
82 - pos = luaL_checknumber(L, 2);
83 + pos = luaL_checklong(L, 2);
84 luaL_argcheck(L, pos < gt_encseq_num_of_sequences(*encseq), 2,
85 "cannot exceed number of sequences");
86 lua_pushnumber(L, gt_encseq_seqstartpos(*encseq, pos));
87 @@ -250,7 +256,7 @@
88 GtEncseq **encseq;
89 GtUword pos;
90 encseq = check_encseq(L, 1);
91 - pos = luaL_checknumber(L, 2);
92 + pos = luaL_checklong(L, 2);
93 luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
94 "cannot exceed total length of encoded sequence");
95 lua_pushnumber(L, gt_encseq_seqnum(*encseq, pos));
96 @@ -279,7 +285,7 @@
97 GtUword seqno, desclen;
98 const char *string;
99 encseq = check_encseq(L, 1);
100 - seqno = luaL_checknumber(L, 2);
101 + seqno = luaL_checklong(L, 2);
102 luaL_argcheck(L, seqno < gt_encseq_num_of_sequences(*encseq), 2,
103 "cannot exceed number of sequences");
104 string = gt_encseq_description(*encseq, &desclen, seqno);
105 @@ -300,7 +306,7 @@
106 GtEncseq **encseq;
107 GtUword fileno;
108 encseq = check_encseq(L, 1);
109 - fileno = luaL_checknumber(L, 2);
110 + fileno = luaL_checklong(L, 2);
111 luaL_argcheck(L, fileno < gt_encseq_num_of_files(*encseq), 2,
112 "cannot exceed number of files");
113 lua_pushnumber(L, gt_encseq_effective_filelength(*encseq, fileno));
114 @@ -312,7 +318,7 @@
115 GtEncseq **encseq;
116 GtUword fileno;
117 encseq = check_encseq(L, 1);
118 - fileno = luaL_checknumber(L, 2);
119 + fileno = luaL_checklong(L, 2);
120 luaL_argcheck(L, fileno < gt_encseq_num_of_files(*encseq), 2,
121 "cannot exceed number of files");
122 lua_pushnumber(L, gt_encseq_filestartpos(*encseq, fileno));
123 @@ -324,7 +330,7 @@
124 GtEncseq **encseq;
125 GtUword pos;
126 encseq = check_encseq(L, 1);
127 - pos = luaL_checknumber(L, 2);
128 + pos = luaL_checklong(L, 2);
129 luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
130 "cannot exceed total length of encoded sequence");
131 lua_pushnumber(L, gt_encseq_filenum(*encseq, pos));
132 @@ -397,8 +403,10 @@
133 GtUword startpos;
134 GtReadmode readmode;
135 encseq = check_encseq(L, 1);
136 - readmode = luaL_checknumber(L, 2);
137 - startpos = luaL_checknumber(L, 3);
138 + readmode = luaL_checklong(L, 2);
139 + startpos = luaL_checklong(L, 3);
140 + luaL_argcheck(L, readmode <= 3, 2,
141 + "invalid readmode value, must be <= 3");
142 luaL_argcheck(L, startpos < gt_encseq_total_length(*encseq), 3,
143 "cannot exceed total length of encoded sequence");
144 reader = gt_encseq_create_reader_with_readmode(*encseq, readmode, startpos);
145 --- a/src/gtlua/mathsupport_lua.c
146 +++ b/src/gtlua/mathsupport_lua.c
147 @@ -21,7 +21,7 @@
148
149 static int gt_lua_mathsupport_rand_max(lua_State *L)
150 {
151 - GtUword max = luaL_checknumber(L, 1);
152 + GtUword max = luaL_checklong(L, 1);
153
154 lua_pushnumber(L, gt_rand_max(max));
155 return 1;
156 --- a/src/match/eis-bwtseq.c
157 +++ b/src/match/eis-bwtseq.c
158 @@ -473,7 +473,7 @@
159 CONTEXT_INTERVAL = 128,
160 };
161
162 -int
163 +enum verifyBWTSeqErrCode
164 gt_BWTSeqVerifyIntegrity(BWTSeq *bwtSeq, const char *projectName,
165 int checkFlags,
166 GtUword tickPrint, FILE *fp,
167 --- a/src/tools/gt_tir.c
168 +++ b/src/tools/gt_tir.c
169 @@ -394,9 +394,9 @@
170 GtNodeVisitor *pdom_v;
171 ms = gt_pdom_model_set_new(arguments->hmm_files, err);
172 if (ms != NULL) {
173 - pdom_v = gt_ltrdigest_pdom_visitor_new(ms, arguments->cutoff,
174 + pdom_v = gt_ltrdigest_pdom_visitor_new(ms, arguments->evalue_cutoff,
175 arguments->chain_max_gap_length,
176 - arguments->evalue_cutoff, rmap,
177 + arguments->cutoff, rmap,
178 err);
179 if (pdom_v == NULL)
180 had_err = -1;
181 --- a/testdata/gtscripts/encseq.lua
182 +++ b/testdata/gtscripts/encseq.lua
183 @@ -60,6 +60,9 @@
184 rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 100, 0)
185 assert(not rval)
186 assert(string.find(err, "cannot exceed"))
187 + rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 10, 6)
188 + assert(not rval)
189 + assert(string.find(err, "invalid readmode"))
190 end
191
192 function run_test_seq_startpos(es)
193 @@ -99,6 +102,9 @@
194 rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
195 assert(not rval)
196 assert(string.find(err, "cannot exceed"))
197 + rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 10, 6)
198 + assert(not rval)
199 + assert(string.find(err, "invalid readmode"))
200 end
201
202 function run_test_file_length_protein(es)
203 @@ -128,7 +134,7 @@
204 rval, err = pcall(GenomeTools_encseq.extract_encoded, es, 300, 500)
205 assert(not rval)
206 assert(string.find(err, "cannot exceed"))
207 -
208 +
209 end
210
211 function run_test_seq_substr_decoded(es, seq1, seq2)
212 @@ -168,7 +174,10 @@
213 rval, err = pcall(GenomeTools_encseq.create_reader_with_readmode, es, 0, 300)
214 assert(not rval)
215 assert(string.find(err, "cannot exceed"))
216 -end
217 + rval, err = pcall(GenomeTools_encseq.create_reader_with_readmode, es, 7, 3)
218 + assert(not rval)
219 + assert(string.find(err, "invalid readmode"))
220 +end
221
222 ee = gt.encseq_encoder_new()
223 ee:encode({dnaseqfile}, "dnaseqfile")
+0
-53
debian/patches/use-pkgconfig less more
0 From afaed82084071e9d11663b7ce593fa83e6eabbe5 Mon Sep 17 00:00:00 2001
1 From: Justus Winter <justus@gnupg.org>
2 Date: Fri, 19 Feb 2016 14:06:41 +0100
3 Subject: [PATCH 1/6] Makefile: Drop spurious '$(3)'
4
5 * Makefile: Drop spurious '$(3)', likely a left-over from copying
6 'COMPILE_template'.
7 ---
8 Makefile | 4 ++--
9 1 file changed, 2 insertions(+), 2 deletions(-)
10
11 --- /dev/null
12 +++ b/src/external/lpeg-0.10.2/lua-lpeg.h
13 @@ -0,0 +1,39 @@
14 +/*
15 +** $Id: lpeg.h,v 1.1 2009/12/23 16:15:36 roberto Exp $
16 +** LPeg - PEG pattern matching for Lua
17 +** Copyright 2009, Lua.org & PUC-Rio (see 'lpeg.html' for license)
18 +** written by Roberto Ierusalimschy
19 +*/
20 +
21 +#ifndef lpeg_h
22 +#define lpeg_h
23 +
24 +#include "lua.h"
25 +
26 +int luaopen_lpeg (lua_State *L);
27 +
28 +#define KEYNEWPATT "lpeg.newpf"
29 +
30 +
31 +/*
32 +** type of extension functions that define new "patterns" for LPEG
33 +** It should return the new current position or NULL if match fails
34 +*/
35 +typedef const char *(*PattFunc) (const char *s, /* current position */
36 + const char *e, /* string end */
37 + const char *o, /* string start */
38 + const void *ud); /* user data */
39 +
40 +/*
41 +** function to create new patterns based on 'PattFunc' functions.
42 +** This function is available at *registry[KEYNEWPATT]. (Notice
43 +** the extra indirection; the userdata at the registry points to
44 +** a variable that points to the function. In ANSI C a void* cannot
45 +** point to a function.)
46 +*/
47 +typedef void (*Newpf) (lua_State *L,
48 + PattFunc f, /* pattern */
49 + const void *ud, /* (user) data to be passed to 'f' */
50 + size_t l); /* size of data to be passed to 'f' */
51 +
52 +#endif