finishm 0.0.1
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- data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
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- data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
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- data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
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- data/lib/assembly/a_b_visualiser.rb +169 -0
- data/lib/assembly/acyclic_connection_finder.rb +81 -0
- data/lib/assembly/all_orfs.rb +615 -0
- data/lib/assembly/bad_format_writer.rb +46 -0
- data/lib/assembly/bam_probe_read_selector.rb +48 -0
- data/lib/assembly/bubbly_assembler.rb +842 -0
- data/lib/assembly/c_probe_node_finder.rb +38 -0
- data/lib/assembly/connection_interpreter.rb +350 -0
- data/lib/assembly/contig_printer.rb +400 -0
- data/lib/assembly/coverage_based_graph_filter.rb +68 -0
- data/lib/assembly/depth_first_search.rb +63 -0
- data/lib/assembly/dijkstra.rb +216 -0
- data/lib/assembly/fluffer.rb +253 -0
- data/lib/assembly/graph_explorer.rb +85 -0
- data/lib/assembly/graph_generator.rb +315 -0
- data/lib/assembly/height_finder.rb +355 -0
- data/lib/assembly/hybrid_velvet_graph.rb +70 -0
- data/lib/assembly/input_genome.rb +182 -0
- data/lib/assembly/kmer_coverage_based_path_filter.rb +65 -0
- data/lib/assembly/node_finder.rb +171 -0
- data/lib/assembly/oriented_node_trail.rb +507 -0
- data/lib/assembly/paired_end_assembler.rb +53 -0
- data/lib/assembly/paired_end_neighbour_finder.rb +176 -0
- data/lib/assembly/probed_graph.rb +105 -0
- data/lib/assembly/read_input.rb +79 -0
- data/lib/assembly/read_to_node.rb +37 -0
- data/lib/assembly/scaffold_breaker.rb +126 -0
- data/lib/assembly/sequence_hasher.rb +71 -0
- data/lib/assembly/single_coherent_paths_between_nodes.rb +533 -0
- data/lib/assembly/single_coherent_wanderer.rb +261 -0
- data/lib/assembly/single_ended_assembler.rb +441 -0
- data/lib/assembly/velvet_c_binding.rb +54 -0
- data/lib/assembly/velvet_graph_sequence_extractor.rb +123 -0
- data/lib/external/VERSION +1 -0
- data/lib/finishm/assemble.rb +224 -0
- data/lib/finishm/explore.rb +217 -0
- data/lib/finishm/finisher.rb +303 -0
- data/lib/finishm/fluff.rb +122 -0
- data/lib/finishm/gapfiller.rb +325 -0
- data/lib/finishm/orfs_finder.rb +88 -0
- data/lib/finishm/path_counter.rb +90 -0
- data/lib/finishm/primers.rb +425 -0
- data/lib/finishm/primers_check.rb +176 -0
- data/lib/finishm/roundup.rb +344 -0
- data/lib/finishm/sequence.rb +142 -0
- data/lib/finishm/visualise.rb +430 -0
- data/lib/finishm/wander.rb +270 -0
- data/lib/kmer_abundance_pattern.rb +79 -0
- data/lib/kmer_multi_abundance_file.rb +48 -0
- data/lib/oligo_designer.rb +88 -0
- data/lib/priner.rb +66 -0
- data/spec/acyclic_connection_finder_spec.rb +551 -0
- data/spec/all_orfs_spec.rb +443 -0
- data/spec/assemble_spec.rb +186 -0
- data/spec/bubbly_assembler_spec.rb +707 -0
- data/spec/c_node_finder_spec.rb +58 -0
- data/spec/connection_interpreter_spec.rb +284 -0
- data/spec/contig_printer_spec.rb +291 -0
- data/spec/coverage_based_graph_filter_spec.rb +102 -0
- data/spec/data/6_3e4e5e6e.1vANME.bam +0 -0
- data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
- data/spec/data/acyclic_connection_finder/1/probes.fa +5 -0
- data/spec/data/acyclic_connection_finder/1/random1.fa +2 -0
- data/spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz +0 -0
- data/spec/data/acyclic_connection_finder/1/random2.fa +2 -0
- data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz +0 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa +39 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa +39 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz +0 -0
- data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 +220 -0
- data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 +220 -0
- data/spec/data/assembly_visualiser/Graph +46 -0
- data/spec/data/assembly_visualiser/start_kmers1 +2 -0
- data/spec/data/bands.csv +1 -0
- data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq +0 -0
- data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names +544 -0
- data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
- data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
- data/spec/data/c_probe_node_finder/1/Log +756 -0
- data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
- data/spec/data/c_probe_node_finder/1/Roadmaps +2009 -0
- data/spec/data/c_probe_node_finder/1/contigs.fa +29 -0
- data/spec/data/c_probe_node_finder/1/stats.txt +6 -0
- data/spec/data/contig_printer/1/HOWTO_RECREATE +17 -0
- data/spec/data/contig_printer/1/contigs.fa +4 -0
- data/spec/data/contig_printer/1/seq.fa +2408 -0
- data/spec/data/contig_printer/1/seq.fa.svg +153 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Graph2 +2953 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/LastGraph +2953 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Log +21 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/PreGraph +27 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Sequences +3612 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/stats.txt +14 -0
- data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam +0 -0
- data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai +0 -0
- data/spec/data/contig_printer/1/seq.node12.fa +4 -0
- data/spec/data/contig_printer/1/seq1_1to550.fa +2 -0
- data/spec/data/contig_printer/1/seq2_1to550.fa +2 -0
- data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
- data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
- data/spec/data/explore/1/HOWTO_RECREATE.txt +6 -0
- data/spec/data/explore/1/a.fa +2 -0
- data/spec/data/explore/1/seq1_and_a.fa +3 -0
- data/spec/data/explore/1/seq2.fa +2 -0
- data/spec/data/fluff/1/2seqs.sammy.fa +12004 -0
- data/spec/data/fluff/1/HOWTO_RECREATE.txt +5 -0
- data/spec/data/fluff/1/seq1.fa +2 -0
- data/spec/data/fluff/1/seq2.fa +2 -0
- data/spec/data/gapfilling/1/reads.fa +171 -0
- data/spec/data/gapfilling/1/trail_with_Ns.fa +5 -0
- data/spec/data/gapfilling/1/velvetAssembly/Graph2 +130 -0
- data/spec/data/gapfilling/1/velvetAssembly/LastGraph +130 -0
- data/spec/data/gapfilling/1/velvetAssembly/Log +199 -0
- data/spec/data/gapfilling/1/velvetAssembly/PreGraph +7 -0
- data/spec/data/gapfilling/1/velvetAssembly/Roadmaps +239 -0
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- data/spec/data/gapfilling/2/reference_part2.fa +4 -0
- data/spec/data/gapfilling/2/sammy_reads.fa.gz +0 -0
- data/spec/data/gapfilling/2/with_gaps.fa +4 -0
- data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
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- data/spec/data/gapfilling/4/HOWTO_recreate +1 -0
- data/spec/data/gapfilling/4/reads.fa.gz +0 -0
- data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -0
- data/spec/data/gapfilling/5/answer.fna +2 -0
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- data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
- data/spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv +2 -0
- data/spec/data/kmers_count1.csv +2 -0
- data/spec/data/kmers_count2.csv +3 -0
- data/spec/data/out +3 -0
- data/spec/data/positive_latching_pair.fa +2 -0
- data/spec/data/primers.csv +4 -0
- data/spec/data/read_selection_by_kmer/blacklist1.txt +1 -0
- data/spec/data/read_selection_by_kmer/input.fasta +6 -0
- data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
- data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
- data/spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt +2 -0
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- data/spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt +3 -0
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- data/spec/dijkstra_spec.rb +143 -0
- data/spec/explore_spec.rb +29 -0
- data/spec/fluffer_spec.rb +155 -0
- data/spec/gapfiller_spec.rb +107 -0
- data/spec/graph_explorer_spec.rb +475 -0
- data/spec/graph_generator_spec.rb +99 -0
- data/spec/height_finder_spec.rb +306 -0
- data/spec/kmer_abundance_pattern_spec.rb +56 -0
- data/spec/kmer_coverage_based_path_filter_spec.rb +73 -0
- data/spec/kmer_profile_finder_spec.rb +38 -0
- data/spec/kmers_count_tabulate_spec.rb +120 -0
- data/spec/oriented_node_trail_spec.rb +221 -0
- data/spec/paired_end_neighbours_spec.rb +126 -0
- data/spec/paths_between_nodes_spec.rb +349 -0
- data/spec/priner_spec.rb +7 -0
- data/spec/read_input_spec.rb +23 -0
- data/spec/read_selection_by_kmer_spec.rb +166 -0
- data/spec/read_to_node_spec.rb +35 -0
- data/spec/roundup_spec.rb +366 -0
- data/spec/scaffold_breaker_spec.rb +144 -0
- data/spec/sequence_spec.rb +43 -0
- data/spec/single_coherent_paths_between_nodes_spec.rb +492 -0
- data/spec/single_coherent_wanderer_spec.rb +120 -0
- data/spec/single_ended_assembler_spec.rb +398 -0
- data/spec/spec_helper.rb +310 -0
- data/spec/velvet_graph_sequence_extractor_spec.rb +80 -0
- data/spec/visualise_spec.rb +105 -0
- data/spec/wander_spec.rb +119 -0
- data/spec/watch_for_changes.sh +16 -0
- data/validation/fasta_compare.rb +72 -0
- data/validation/gapfill_simulate_perfect.rb +108 -0
- metadata +899 -0
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/*
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minizip.c
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Version 1.01e, February 12th, 2005
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Copyright (C) 1998-2005 Gilles Vollant
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <time.h>
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#include <fcntl.h>
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#ifdef unix
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# include <sys/types.h>
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# include <sys/stat.h>
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#else
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# include <direct.h>
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# include <io.h>
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#ifdef WIN32
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uLong filetime(f, tmzip, dt)
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char *f; /* name of file to get info on */
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tm_zip *tmzip; /* return value: access, modific. and creation times */
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uLong *dt; /* dostime */
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{
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{
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HANDLE hFind;
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hFind = FindFirstFile(f,&ff32);
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if (hFind != INVALID_HANDLE_VALUE)
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{
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FileTimeToLocalFileTime(&(ff32.ftLastWriteTime),&ftLocal);
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}
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return ret;
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}
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#else
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|
+
#ifdef unix
|
62
|
+
uLong filetime(f, tmzip, dt)
|
63
|
+
char *f; /* name of file to get info on */
|
64
|
+
tm_zip *tmzip; /* return value: access, modific. and creation times */
|
65
|
+
uLong *dt; /* dostime */
|
66
|
+
{
|
67
|
+
int ret=0;
|
68
|
+
struct stat s; /* results of stat() */
|
69
|
+
struct tm* filedate;
|
70
|
+
time_t tm_t=0;
|
71
|
+
|
72
|
+
if (strcmp(f,"-")!=0)
|
73
|
+
{
|
74
|
+
char name[MAXFILENAME+1];
|
75
|
+
int len = strlen(f);
|
76
|
+
if (len > MAXFILENAME)
|
77
|
+
len = MAXFILENAME;
|
78
|
+
|
79
|
+
strncpy(name, f,MAXFILENAME-1);
|
80
|
+
/* strncpy doesnt append the trailing NULL, of the string is too long. */
|
81
|
+
name[ MAXFILENAME ] = '\0';
|
82
|
+
|
83
|
+
if (name[len - 1] == '/')
|
84
|
+
name[len - 1] = '\0';
|
85
|
+
/* not all systems allow stat'ing a file with / appended */
|
86
|
+
if (stat(name,&s)==0)
|
87
|
+
{
|
88
|
+
tm_t = s.st_mtime;
|
89
|
+
ret = 1;
|
90
|
+
}
|
91
|
+
}
|
92
|
+
filedate = localtime(&tm_t);
|
93
|
+
|
94
|
+
tmzip->tm_sec = filedate->tm_sec;
|
95
|
+
tmzip->tm_min = filedate->tm_min;
|
96
|
+
tmzip->tm_hour = filedate->tm_hour;
|
97
|
+
tmzip->tm_mday = filedate->tm_mday;
|
98
|
+
tmzip->tm_mon = filedate->tm_mon ;
|
99
|
+
tmzip->tm_year = filedate->tm_year;
|
100
|
+
|
101
|
+
return ret;
|
102
|
+
}
|
103
|
+
#else
|
104
|
+
uLong filetime(f, tmzip, dt)
|
105
|
+
char *f; /* name of file to get info on */
|
106
|
+
tm_zip *tmzip; /* return value: access, modific. and creation times */
|
107
|
+
uLong *dt; /* dostime */
|
108
|
+
{
|
109
|
+
return 0;
|
110
|
+
}
|
111
|
+
#endif
|
112
|
+
#endif
|
113
|
+
|
114
|
+
|
115
|
+
|
116
|
+
|
117
|
+
int check_exist_file(filename)
|
118
|
+
const char* filename;
|
119
|
+
{
|
120
|
+
FILE* ftestexist;
|
121
|
+
int ret = 1;
|
122
|
+
ftestexist = fopen(filename,"rb");
|
123
|
+
if (ftestexist==NULL)
|
124
|
+
ret = 0;
|
125
|
+
else
|
126
|
+
fclose(ftestexist);
|
127
|
+
return ret;
|
128
|
+
}
|
129
|
+
|
130
|
+
void do_banner()
|
131
|
+
{
|
132
|
+
printf("MiniZip 1.01b, demo of zLib + Zip package written by Gilles Vollant\n");
|
133
|
+
printf("more info at http://www.winimage.com/zLibDll/unzip.html\n\n");
|
134
|
+
}
|
135
|
+
|
136
|
+
void do_help()
|
137
|
+
{
|
138
|
+
printf("Usage : minizip [-o] [-a] [-0 to -9] [-p password] file.zip [files_to_add]\n\n" \
|
139
|
+
" -o Overwrite existing file.zip\n" \
|
140
|
+
" -a Append to existing file.zip\n" \
|
141
|
+
" -0 Store only\n" \
|
142
|
+
" -1 Compress faster\n" \
|
143
|
+
" -9 Compress better\n\n");
|
144
|
+
}
|
145
|
+
|
146
|
+
/* calculate the CRC32 of a file,
|
147
|
+
because to encrypt a file, we need known the CRC32 of the file before */
|
148
|
+
int getFileCrc(const char* filenameinzip,void*buf,unsigned long size_buf,unsigned long* result_crc)
|
149
|
+
{
|
150
|
+
unsigned long calculate_crc=0;
|
151
|
+
int err=ZIP_OK;
|
152
|
+
FILE * fin = fopen(filenameinzip,"rb");
|
153
|
+
unsigned long size_read = 0;
|
154
|
+
unsigned long total_read = 0;
|
155
|
+
if (fin==NULL)
|
156
|
+
{
|
157
|
+
err = ZIP_ERRNO;
|
158
|
+
}
|
159
|
+
|
160
|
+
if (err == ZIP_OK)
|
161
|
+
do
|
162
|
+
{
|
163
|
+
err = ZIP_OK;
|
164
|
+
size_read = (int)fread(buf,1,size_buf,fin);
|
165
|
+
if (size_read < size_buf)
|
166
|
+
if (feof(fin)==0)
|
167
|
+
{
|
168
|
+
printf("error in reading %s\n",filenameinzip);
|
169
|
+
err = ZIP_ERRNO;
|
170
|
+
}
|
171
|
+
|
172
|
+
if (size_read>0)
|
173
|
+
calculate_crc = crc32(calculate_crc,buf,size_read);
|
174
|
+
total_read += size_read;
|
175
|
+
|
176
|
+
} while ((err == ZIP_OK) && (size_read>0));
|
177
|
+
|
178
|
+
if (fin)
|
179
|
+
fclose(fin);
|
180
|
+
|
181
|
+
*result_crc=calculate_crc;
|
182
|
+
printf("file %s crc %x\n",filenameinzip,calculate_crc);
|
183
|
+
return err;
|
184
|
+
}
|
185
|
+
|
186
|
+
int main(argc,argv)
|
187
|
+
int argc;
|
188
|
+
char *argv[];
|
189
|
+
{
|
190
|
+
int i;
|
191
|
+
int opt_overwrite=0;
|
192
|
+
int opt_compress_level=Z_DEFAULT_COMPRESSION;
|
193
|
+
int zipfilenamearg = 0;
|
194
|
+
char filename_try[MAXFILENAME+16];
|
195
|
+
int zipok;
|
196
|
+
int err=0;
|
197
|
+
int size_buf=0;
|
198
|
+
void* buf=NULL;
|
199
|
+
const char* password=NULL;
|
200
|
+
|
201
|
+
|
202
|
+
do_banner();
|
203
|
+
if (argc==1)
|
204
|
+
{
|
205
|
+
do_help();
|
206
|
+
return 0;
|
207
|
+
}
|
208
|
+
else
|
209
|
+
{
|
210
|
+
for (i=1;i<argc;i++)
|
211
|
+
{
|
212
|
+
if ((*argv[i])=='-')
|
213
|
+
{
|
214
|
+
const char *p=argv[i]+1;
|
215
|
+
|
216
|
+
while ((*p)!='\0')
|
217
|
+
{
|
218
|
+
char c=*(p++);;
|
219
|
+
if ((c=='o') || (c=='O'))
|
220
|
+
opt_overwrite = 1;
|
221
|
+
if ((c=='a') || (c=='A'))
|
222
|
+
opt_overwrite = 2;
|
223
|
+
if ((c>='0') && (c<='9'))
|
224
|
+
opt_compress_level = c-'0';
|
225
|
+
|
226
|
+
if (((c=='p') || (c=='P')) && (i+1<argc))
|
227
|
+
{
|
228
|
+
password=argv[i+1];
|
229
|
+
i++;
|
230
|
+
}
|
231
|
+
}
|
232
|
+
}
|
233
|
+
else
|
234
|
+
if (zipfilenamearg == 0)
|
235
|
+
zipfilenamearg = i ;
|
236
|
+
}
|
237
|
+
}
|
238
|
+
|
239
|
+
size_buf = WRITEBUFFERSIZE;
|
240
|
+
buf = (void*)malloc(size_buf);
|
241
|
+
if (buf==NULL)
|
242
|
+
{
|
243
|
+
printf("Error allocating memory\n");
|
244
|
+
return ZIP_INTERNALERROR;
|
245
|
+
}
|
246
|
+
|
247
|
+
if (zipfilenamearg==0)
|
248
|
+
zipok=0;
|
249
|
+
else
|
250
|
+
{
|
251
|
+
int i,len;
|
252
|
+
int dot_found=0;
|
253
|
+
|
254
|
+
zipok = 1 ;
|
255
|
+
strncpy(filename_try, argv[zipfilenamearg],MAXFILENAME-1);
|
256
|
+
/* strncpy doesnt append the trailing NULL, of the string is too long. */
|
257
|
+
filename_try[ MAXFILENAME ] = '\0';
|
258
|
+
|
259
|
+
len=(int)strlen(filename_try);
|
260
|
+
for (i=0;i<len;i++)
|
261
|
+
if (filename_try[i]=='.')
|
262
|
+
dot_found=1;
|
263
|
+
|
264
|
+
if (dot_found==0)
|
265
|
+
strcat(filename_try,".zip");
|
266
|
+
|
267
|
+
if (opt_overwrite==2)
|
268
|
+
{
|
269
|
+
/* if the file don't exist, we not append file */
|
270
|
+
if (check_exist_file(filename_try)==0)
|
271
|
+
opt_overwrite=1;
|
272
|
+
}
|
273
|
+
else
|
274
|
+
if (opt_overwrite==0)
|
275
|
+
if (check_exist_file(filename_try)!=0)
|
276
|
+
{
|
277
|
+
char rep=0;
|
278
|
+
do
|
279
|
+
{
|
280
|
+
char answer[128];
|
281
|
+
int ret;
|
282
|
+
printf("The file %s exists. Overwrite ? [y]es, [n]o, [a]ppend : ",filename_try);
|
283
|
+
ret = scanf("%1s",answer);
|
284
|
+
if (ret != 1)
|
285
|
+
{
|
286
|
+
exit(EXIT_FAILURE);
|
287
|
+
}
|
288
|
+
rep = answer[0] ;
|
289
|
+
if ((rep>='a') && (rep<='z'))
|
290
|
+
rep -= 0x20;
|
291
|
+
}
|
292
|
+
while ((rep!='Y') && (rep!='N') && (rep!='A'));
|
293
|
+
if (rep=='N')
|
294
|
+
zipok = 0;
|
295
|
+
if (rep=='A')
|
296
|
+
opt_overwrite = 2;
|
297
|
+
}
|
298
|
+
}
|
299
|
+
|
300
|
+
if (zipok==1)
|
301
|
+
{
|
302
|
+
zipFile zf;
|
303
|
+
int errclose;
|
304
|
+
# ifdef USEWIN32IOAPI
|
305
|
+
zlib_filefunc_def ffunc;
|
306
|
+
fill_win32_filefunc(&ffunc);
|
307
|
+
zf = zipOpen2(filename_try,(opt_overwrite==2) ? 2 : 0,NULL,&ffunc);
|
308
|
+
# else
|
309
|
+
zf = zipOpen(filename_try,(opt_overwrite==2) ? 2 : 0);
|
310
|
+
# endif
|
311
|
+
|
312
|
+
if (zf == NULL)
|
313
|
+
{
|
314
|
+
printf("error opening %s\n",filename_try);
|
315
|
+
err= ZIP_ERRNO;
|
316
|
+
}
|
317
|
+
else
|
318
|
+
printf("creating %s\n",filename_try);
|
319
|
+
|
320
|
+
for (i=zipfilenamearg+1;(i<argc) && (err==ZIP_OK);i++)
|
321
|
+
{
|
322
|
+
if (!((((*(argv[i]))=='-') || ((*(argv[i]))=='/')) &&
|
323
|
+
((argv[i][1]=='o') || (argv[i][1]=='O') ||
|
324
|
+
(argv[i][1]=='a') || (argv[i][1]=='A') ||
|
325
|
+
(argv[i][1]=='p') || (argv[i][1]=='P') ||
|
326
|
+
((argv[i][1]>='0') || (argv[i][1]<='9'))) &&
|
327
|
+
(strlen(argv[i]) == 2)))
|
328
|
+
{
|
329
|
+
FILE * fin;
|
330
|
+
int size_read;
|
331
|
+
const char* filenameinzip = argv[i];
|
332
|
+
zip_fileinfo zi;
|
333
|
+
unsigned long crcFile=0;
|
334
|
+
|
335
|
+
zi.tmz_date.tm_sec = zi.tmz_date.tm_min = zi.tmz_date.tm_hour =
|
336
|
+
zi.tmz_date.tm_mday = zi.tmz_date.tm_mon = zi.tmz_date.tm_year = 0;
|
337
|
+
zi.dosDate = 0;
|
338
|
+
zi.internal_fa = 0;
|
339
|
+
zi.external_fa = 0;
|
340
|
+
filetime(filenameinzip,&zi.tmz_date,&zi.dosDate);
|
341
|
+
|
342
|
+
/*
|
343
|
+
err = zipOpenNewFileInZip(zf,filenameinzip,&zi,
|
344
|
+
NULL,0,NULL,0,NULL / * comment * /,
|
345
|
+
(opt_compress_level != 0) ? Z_DEFLATED : 0,
|
346
|
+
opt_compress_level);
|
347
|
+
*/
|
348
|
+
if ((password != NULL) && (err==ZIP_OK))
|
349
|
+
err = getFileCrc(filenameinzip,buf,size_buf,&crcFile);
|
350
|
+
|
351
|
+
err = zipOpenNewFileInZip3(zf,filenameinzip,&zi,
|
352
|
+
NULL,0,NULL,0,NULL /* comment*/,
|
353
|
+
(opt_compress_level != 0) ? Z_DEFLATED : 0,
|
354
|
+
opt_compress_level,0,
|
355
|
+
/* -MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY, */
|
356
|
+
-MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY,
|
357
|
+
password,crcFile);
|
358
|
+
|
359
|
+
if (err != ZIP_OK)
|
360
|
+
printf("error in opening %s in zipfile\n",filenameinzip);
|
361
|
+
else
|
362
|
+
{
|
363
|
+
fin = fopen(filenameinzip,"rb");
|
364
|
+
if (fin==NULL)
|
365
|
+
{
|
366
|
+
err=ZIP_ERRNO;
|
367
|
+
printf("error in opening %s for reading\n",filenameinzip);
|
368
|
+
}
|
369
|
+
}
|
370
|
+
|
371
|
+
if (err == ZIP_OK)
|
372
|
+
do
|
373
|
+
{
|
374
|
+
err = ZIP_OK;
|
375
|
+
size_read = (int)fread(buf,1,size_buf,fin);
|
376
|
+
if (size_read < size_buf)
|
377
|
+
if (feof(fin)==0)
|
378
|
+
{
|
379
|
+
printf("error in reading %s\n",filenameinzip);
|
380
|
+
err = ZIP_ERRNO;
|
381
|
+
}
|
382
|
+
|
383
|
+
if (size_read>0)
|
384
|
+
{
|
385
|
+
err = zipWriteInFileInZip (zf,buf,size_read);
|
386
|
+
if (err<0)
|
387
|
+
{
|
388
|
+
printf("error in writing %s in the zipfile\n",
|
389
|
+
filenameinzip);
|
390
|
+
}
|
391
|
+
|
392
|
+
}
|
393
|
+
} while ((err == ZIP_OK) && (size_read>0));
|
394
|
+
|
395
|
+
if (fin)
|
396
|
+
fclose(fin);
|
397
|
+
|
398
|
+
if (err<0)
|
399
|
+
err=ZIP_ERRNO;
|
400
|
+
else
|
401
|
+
{
|
402
|
+
err = zipCloseFileInZip(zf);
|
403
|
+
if (err!=ZIP_OK)
|
404
|
+
printf("error in closing %s in the zipfile\n",
|
405
|
+
filenameinzip);
|
406
|
+
}
|
407
|
+
}
|
408
|
+
}
|
409
|
+
errclose = zipClose(zf,NULL);
|
410
|
+
if (errclose != ZIP_OK)
|
411
|
+
printf("error in closing %s\n",filename_try);
|
412
|
+
}
|
413
|
+
else
|
414
|
+
{
|
415
|
+
do_help();
|
416
|
+
}
|
417
|
+
|
418
|
+
free(buf);
|
419
|
+
return 0;
|
420
|
+
}
|
@@ -0,0 +1,281 @@
|
|
1
|
+
/*
|
2
|
+
Additional tools for Minizip
|
3
|
+
Code: Xavier Roche '2004
|
4
|
+
License: Same as ZLIB (www.gzip.org)
|
5
|
+
*/
|
6
|
+
|
7
|
+
/* Code */
|
8
|
+
#include <stdio.h>
|
9
|
+
#include <stdlib.h>
|
10
|
+
#include <string.h>
|
11
|
+
#include "zlib.h"
|
12
|
+
#include "unzip.h"
|
13
|
+
|
14
|
+
#define READ_8(adr) ((unsigned char)*(adr))
|
15
|
+
#define READ_16(adr) ( READ_8(adr) | (READ_8(adr+1) << 8) )
|
16
|
+
#define READ_32(adr) ( READ_16(adr) | (READ_16((adr)+2) << 16) )
|
17
|
+
|
18
|
+
#define WRITE_8(buff, n) do { \
|
19
|
+
*((unsigned char*)(buff)) = (unsigned char) ((n) & 0xff); \
|
20
|
+
} while(0)
|
21
|
+
#define WRITE_16(buff, n) do { \
|
22
|
+
WRITE_8((unsigned char*)(buff), n); \
|
23
|
+
WRITE_8(((unsigned char*)(buff)) + 1, (n) >> 8); \
|
24
|
+
} while(0)
|
25
|
+
#define WRITE_32(buff, n) do { \
|
26
|
+
WRITE_16((unsigned char*)(buff), (n) & 0xffff); \
|
27
|
+
WRITE_16((unsigned char*)(buff) + 2, (n) >> 16); \
|
28
|
+
} while(0)
|
29
|
+
|
30
|
+
extern int ZEXPORT unzRepair(file, fileOut, fileOutTmp, nRecovered, bytesRecovered)
|
31
|
+
const char* file;
|
32
|
+
const char* fileOut;
|
33
|
+
const char* fileOutTmp;
|
34
|
+
uLong* nRecovered;
|
35
|
+
uLong* bytesRecovered;
|
36
|
+
{
|
37
|
+
int err = Z_OK;
|
38
|
+
FILE* fpZip = fopen(file, "rb");
|
39
|
+
FILE* fpOut = fopen(fileOut, "wb");
|
40
|
+
FILE* fpOutCD = fopen(fileOutTmp, "wb");
|
41
|
+
if (fpZip != NULL && fpOut != NULL) {
|
42
|
+
int entries = 0;
|
43
|
+
uLong totalBytes = 0;
|
44
|
+
char header[30];
|
45
|
+
char filename[256];
|
46
|
+
char extra[1024];
|
47
|
+
int offset = 0;
|
48
|
+
int offsetCD = 0;
|
49
|
+
while ( fread(header, 1, 30, fpZip) == 30 ) {
|
50
|
+
int currentOffset = offset;
|
51
|
+
|
52
|
+
/* File entry */
|
53
|
+
if (READ_32(header) == 0x04034b50) {
|
54
|
+
unsigned int version = READ_16(header + 4);
|
55
|
+
unsigned int gpflag = READ_16(header + 6);
|
56
|
+
unsigned int method = READ_16(header + 8);
|
57
|
+
unsigned int filetime = READ_16(header + 10);
|
58
|
+
unsigned int filedate = READ_16(header + 12);
|
59
|
+
unsigned int crc = READ_32(header + 14); /* crc */
|
60
|
+
unsigned int cpsize = READ_32(header + 18); /* compressed size */
|
61
|
+
unsigned int uncpsize = READ_32(header + 22); /* uncompressed sz */
|
62
|
+
unsigned int fnsize = READ_16(header + 26); /* file name length */
|
63
|
+
unsigned int extsize = READ_16(header + 28); /* extra field length */
|
64
|
+
filename[0] = extra[0] = '\0';
|
65
|
+
|
66
|
+
/* Header */
|
67
|
+
if (fwrite(header, 1, 30, fpOut) == 30) {
|
68
|
+
offset += 30;
|
69
|
+
} else {
|
70
|
+
err = Z_ERRNO;
|
71
|
+
break;
|
72
|
+
}
|
73
|
+
|
74
|
+
/* Filename */
|
75
|
+
if (fnsize > 0) {
|
76
|
+
if (fread(filename, 1, fnsize, fpZip) == fnsize) {
|
77
|
+
if (fwrite(filename, 1, fnsize, fpOut) == fnsize) {
|
78
|
+
offset += fnsize;
|
79
|
+
} else {
|
80
|
+
err = Z_ERRNO;
|
81
|
+
break;
|
82
|
+
}
|
83
|
+
} else {
|
84
|
+
err = Z_ERRNO;
|
85
|
+
break;
|
86
|
+
}
|
87
|
+
} else {
|
88
|
+
err = Z_STREAM_ERROR;
|
89
|
+
break;
|
90
|
+
}
|
91
|
+
|
92
|
+
/* Extra field */
|
93
|
+
if (extsize > 0) {
|
94
|
+
if (fread(extra, 1, extsize, fpZip) == extsize) {
|
95
|
+
if (fwrite(extra, 1, extsize, fpOut) == extsize) {
|
96
|
+
offset += extsize;
|
97
|
+
} else {
|
98
|
+
err = Z_ERRNO;
|
99
|
+
break;
|
100
|
+
}
|
101
|
+
} else {
|
102
|
+
err = Z_ERRNO;
|
103
|
+
break;
|
104
|
+
}
|
105
|
+
}
|
106
|
+
|
107
|
+
/* Data */
|
108
|
+
{
|
109
|
+
int dataSize = cpsize;
|
110
|
+
if (dataSize == 0) {
|
111
|
+
dataSize = uncpsize;
|
112
|
+
}
|
113
|
+
if (dataSize > 0) {
|
114
|
+
char* data = malloc(dataSize);
|
115
|
+
if (data != NULL) {
|
116
|
+
if ((int)fread(data, 1, dataSize, fpZip) == dataSize) {
|
117
|
+
if ((int)fwrite(data, 1, dataSize, fpOut) == dataSize) {
|
118
|
+
offset += dataSize;
|
119
|
+
totalBytes += dataSize;
|
120
|
+
} else {
|
121
|
+
err = Z_ERRNO;
|
122
|
+
}
|
123
|
+
} else {
|
124
|
+
err = Z_ERRNO;
|
125
|
+
}
|
126
|
+
free(data);
|
127
|
+
if (err != Z_OK) {
|
128
|
+
break;
|
129
|
+
}
|
130
|
+
} else {
|
131
|
+
err = Z_MEM_ERROR;
|
132
|
+
break;
|
133
|
+
}
|
134
|
+
}
|
135
|
+
}
|
136
|
+
|
137
|
+
/* Central directory entry */
|
138
|
+
{
|
139
|
+
char header[46];
|
140
|
+
char* comment = "";
|
141
|
+
int comsize = (int) strlen(comment);
|
142
|
+
WRITE_32(header, 0x02014b50);
|
143
|
+
WRITE_16(header + 4, version);
|
144
|
+
WRITE_16(header + 6, version);
|
145
|
+
WRITE_16(header + 8, gpflag);
|
146
|
+
WRITE_16(header + 10, method);
|
147
|
+
WRITE_16(header + 12, filetime);
|
148
|
+
WRITE_16(header + 14, filedate);
|
149
|
+
WRITE_32(header + 16, crc);
|
150
|
+
WRITE_32(header + 20, cpsize);
|
151
|
+
WRITE_32(header + 24, uncpsize);
|
152
|
+
WRITE_16(header + 28, fnsize);
|
153
|
+
WRITE_16(header + 30, extsize);
|
154
|
+
WRITE_16(header + 32, comsize);
|
155
|
+
WRITE_16(header + 34, 0); /* disk # */
|
156
|
+
WRITE_16(header + 36, 0); /* int attrb */
|
157
|
+
WRITE_32(header + 38, 0); /* ext attrb */
|
158
|
+
WRITE_32(header + 42, currentOffset);
|
159
|
+
/* Header */
|
160
|
+
if (fwrite(header, 1, 46, fpOutCD) == 46) {
|
161
|
+
offsetCD += 46;
|
162
|
+
|
163
|
+
/* Filename */
|
164
|
+
if (fnsize > 0) {
|
165
|
+
if (fwrite(filename, 1, fnsize, fpOutCD) == fnsize) {
|
166
|
+
offsetCD += fnsize;
|
167
|
+
} else {
|
168
|
+
err = Z_ERRNO;
|
169
|
+
break;
|
170
|
+
}
|
171
|
+
} else {
|
172
|
+
err = Z_STREAM_ERROR;
|
173
|
+
break;
|
174
|
+
}
|
175
|
+
|
176
|
+
/* Extra field */
|
177
|
+
if (extsize > 0) {
|
178
|
+
if (fwrite(extra, 1, extsize, fpOutCD) == extsize) {
|
179
|
+
offsetCD += extsize;
|
180
|
+
} else {
|
181
|
+
err = Z_ERRNO;
|
182
|
+
break;
|
183
|
+
}
|
184
|
+
}
|
185
|
+
|
186
|
+
/* Comment field */
|
187
|
+
if (comsize > 0) {
|
188
|
+
if ((int)fwrite(comment, 1, comsize, fpOutCD) == comsize) {
|
189
|
+
offsetCD += comsize;
|
190
|
+
} else {
|
191
|
+
err = Z_ERRNO;
|
192
|
+
break;
|
193
|
+
}
|
194
|
+
}
|
195
|
+
|
196
|
+
|
197
|
+
} else {
|
198
|
+
err = Z_ERRNO;
|
199
|
+
break;
|
200
|
+
}
|
201
|
+
}
|
202
|
+
|
203
|
+
/* Success */
|
204
|
+
entries++;
|
205
|
+
|
206
|
+
} else {
|
207
|
+
break;
|
208
|
+
}
|
209
|
+
}
|
210
|
+
|
211
|
+
/* Final central directory */
|
212
|
+
{
|
213
|
+
int entriesZip = entries;
|
214
|
+
char header[22];
|
215
|
+
char* comment = ""; // "ZIP File recovered by zlib/minizip/mztools";
|
216
|
+
int comsize = (int) strlen(comment);
|
217
|
+
if (entriesZip > 0xffff) {
|
218
|
+
entriesZip = 0xffff;
|
219
|
+
}
|
220
|
+
WRITE_32(header, 0x06054b50);
|
221
|
+
WRITE_16(header + 4, 0); /* disk # */
|
222
|
+
WRITE_16(header + 6, 0); /* disk # */
|
223
|
+
WRITE_16(header + 8, entriesZip); /* hack */
|
224
|
+
WRITE_16(header + 10, entriesZip); /* hack */
|
225
|
+
WRITE_32(header + 12, offsetCD); /* size of CD */
|
226
|
+
WRITE_32(header + 16, offset); /* offset to CD */
|
227
|
+
WRITE_16(header + 20, comsize); /* comment */
|
228
|
+
|
229
|
+
/* Header */
|
230
|
+
if (fwrite(header, 1, 22, fpOutCD) == 22) {
|
231
|
+
|
232
|
+
/* Comment field */
|
233
|
+
if (comsize > 0) {
|
234
|
+
if ((int)fwrite(comment, 1, comsize, fpOutCD) != comsize) {
|
235
|
+
err = Z_ERRNO;
|
236
|
+
}
|
237
|
+
}
|
238
|
+
|
239
|
+
} else {
|
240
|
+
err = Z_ERRNO;
|
241
|
+
}
|
242
|
+
}
|
243
|
+
|
244
|
+
/* Final merge (file + central directory) */
|
245
|
+
fclose(fpOutCD);
|
246
|
+
if (err == Z_OK) {
|
247
|
+
fpOutCD = fopen(fileOutTmp, "rb");
|
248
|
+
if (fpOutCD != NULL) {
|
249
|
+
int nRead;
|
250
|
+
char buffer[8192];
|
251
|
+
while ( (nRead = (int)fread(buffer, 1, sizeof(buffer), fpOutCD)) > 0) {
|
252
|
+
if ((int)fwrite(buffer, 1, nRead, fpOut) != nRead) {
|
253
|
+
err = Z_ERRNO;
|
254
|
+
break;
|
255
|
+
}
|
256
|
+
}
|
257
|
+
fclose(fpOutCD);
|
258
|
+
}
|
259
|
+
}
|
260
|
+
|
261
|
+
/* Close */
|
262
|
+
fclose(fpZip);
|
263
|
+
fclose(fpOut);
|
264
|
+
|
265
|
+
/* Wipe temporary file */
|
266
|
+
(void)remove(fileOutTmp);
|
267
|
+
|
268
|
+
/* Number of recovered entries */
|
269
|
+
if (err == Z_OK) {
|
270
|
+
if (nRecovered != NULL) {
|
271
|
+
*nRecovered = entries;
|
272
|
+
}
|
273
|
+
if (bytesRecovered != NULL) {
|
274
|
+
*bytesRecovered = totalBytes;
|
275
|
+
}
|
276
|
+
}
|
277
|
+
} else {
|
278
|
+
err = Z_STREAM_ERROR;
|
279
|
+
}
|
280
|
+
return err;
|
281
|
+
}
|