Codebase list vmatch / 1f933a2
add man pages Sascha Steinbiss 4 years ago
13 changed file(s) with 936 addition(s) and 4 deletion(s). Raw diff Collapse all Expand all
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debian/mansrc/chain2dim.1.adoc less more
0 # chain2dim(1)
1
2 ## NAME
3
4 chain2dim - two-dimensional match chaining
5
6 ## SYNOPSIS
7
8 *chain2dim* [options] <matchfile>
9
10 ## OPTIONS
11
12 *-global* <param>::
13 Global chaining. Optional parameter "gc" switches on gap costs (according to
14 L1-model). Optional parameter "ov" means that overlaps between matches are
15 allowed.
16
17 *-local* <param>::
18 Compute local chains (according to L1-model).
19 If no parameter is given, compute local chains with maximum score.
20 If parameter is given, this must be a positive number optionally followed by
21 the character b or p. If only the number, say k, is given, this is the
22 minimum score of the chains output.
23 If a number is followed by character b, then output all chains with the
24 largest k scores. If a number is followed by character p, then output all
25 chains with scores at most k percent away from the best score.
26
27 *-wf* <factor>::
28 Specify weight factor > 0.0 to obtain the score of a fragment. Requires one
29 of the options *-local*, *-global gc* or *-global ov*.
30
31 *-maxgap* <width>::
32 Maximal width of gap in chain.
33
34 *-outprefix* <prefix>::
35 Specify prefix of files to output chains.
36
37 *-withinborders*::
38 Only compute chains which do not cross sequence borders (not possible for
39 matches in open format).
40
41 *-thread* <keywords...>::
42 Thread the chains, i.e. close the gaps. Accepts an optional list of keywords
43 "minlen1 minlen2 maxerror1 maxerror2", each followed by a number specifies
44 the minimum length and the maximum error rate of thread.
45 1 refers to match instance in indexed sequence, 2 refers to matching
46 instance in query.
47
48 *-silent*::
49 Do not output the chains and only report their lengths and scores.
50
51 *-v*::
52 Be verbose.
53
54 *-version*::
55 Show the version of the Vmatch package.
56
57 *-help*::
58 Show help.
59
60 ## SEE ALSO
61
62 vmatch(1)
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debian/mansrc/matchcluster.1.adoc less more
0 # matchcluster (1)
1
2 ## NAME
3
4 matchcluster - match clustering
5
6 ## SYNOPSIS
7
8 *matchcluster* [options] <matchfile>
9
10 ## OPTIONS
11
12 *-erate* <value>::
13 Specify maximum error rate in range [0,100] for similarity clustering.
14
15 *-gapsize* <size>::
16 Specify maximum gap size for gap clustering.
17
18 *-overlap* <percentage>::
19 Specify minimum percentage of overlap for overlap clustering.
20
21 *-outprefix* <string>::
22 Specify prefix of files to output clusters.
23
24 *-version*::
25 Show the version of the Vmatch package.
26
27 *-help*::
28 Show help.
29
30 ## SEE ALSO
31
32 vmatch(1)
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debian/mansrc/mkdna6idx.1.adoc less more
0 # mkdna6idx(1)
1
2 ## NAME
3
4 mkdna6idx - generate a six frame translation index
5
6 ## SYNOPSIS
7
8 *mkdna6idx* [options] <indexname>
9
10 ## DESCRIPTION
11
12 *mkdna6idx* is very similar to *mkvtree*. While *mkvtree* can handle sequences
13 over arbitrary alphabets, *mkdna6idx* requires DNA-sequences as input. It
14 generates two indices, namely:
15
16 * A flat index "indexname" for the the given DNA sequences. It mainly consists
17 of the two files "indexname.tis" and "indexname.ois". This index is mainly
18 used for output purpose.
19 * An index "indexname.6fr" for the given DNA sequences translated in all six
20 reading frames.This is used for computing the matches.
21
22 Please also see the Vmatch manual for a more detailed explanation of the usage.
23
24 ## OPTIONS
25
26 *-db* <file>::
27 Specify database files (mandatory).
28
29 *-smap* <file>::
30 Specify file containing a symbol mapping. This describes the grouping of
31 symbols. It is possible to set the environment variable MKVTREESMAPDIR
32 to the path where these files can be found.
33
34 *-transnum* <table>::
35 Perform six frame translation. Specify codon translation table by a number
36 in the range [1,23] except for 7, 8, 17, 18, 19 and 20; (default is 1):
37
38 1 Standard
39 2 Vertebrate Mitochondrial
40 3 Yeast Mitochondrial
41 4 Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
42 5 Invertebrate Mitochondrial
43 6 Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
44 9 Echinoderm Mitochondrial
45 10 Euplotid Nuclear
46 11 Bacterial
47 12 Alternative Yeast Nuclear
48 13 Ascidian Mitochondrial
49 14 Flatworm Mitochondrial
50 15 Blepharisma Macronuclear
51 16 Chlorophycean Mitochondrial
52 21 Trematode Mitochondrial
53 22 Scenedesmus Obliquus Mitochondrial
54 23 Thraustochytrium Mitochondrial
55
56 *-indexname* <string>::
57 Specify name for index to be generated.
58
59 *-cpl*::
60 Use reverse complement of the input sequence.
61
62 *-tis*::
63 Output transformed input sequences (tistab) to file.
64
65 *-ois*::
66 Output original input sequences (oistab) to file.
67
68 *-maxdepth* <len>::
69 Restrict the sorting to prefixes of the given length.
70
71 *-v*::
72 Verbose mode.
73
74 *-version*::
75 Show the version of the Vmatch package
76
77 *-help*::
78 Show help.
79
80 ## SEE ALSO
81
82 mkvtree(1)
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debian/mansrc/mkvtree.1.adoc less more
0 # mkvtree(1)
1
2 ## NAME
3
4 mkvtree - construct index for sequence
5
6 ## SYNOPSIS
7
8 *mkvtree* [options]
9
10 ## DESCRIPTION
11
12 The program *mkvtree* constructs an index for a given set of sequences. These
13 are given as a list of input files. The sequences are referred to as database
14 sequences. They can be over any given alphabet. The alphabet can be the DNA
15 alphabet, or the protein alphabet, or any other alphabet consisting of
16 printable characters. An alphabet is specified by a file storing a symbol
17 mapping. The index consists of several files, the index files. Each such file
18 stores a different table. The user specifies which tables (i.e. which part of
19 the index) is written to a file, using one of eight output options, or a
20 single option specifying that all tables are written to file.
21
22 We support the following formats for the input files. They are recognized
23 according to the first non-whitespace symbol in the file.
24
25 * multiple FASTA format: If the file begins with the symbol ">", then this
26 file is considered to be a file in multiple FASTA format (i.e. it contains
27 one or more sequences). Each line starting with the symbol ">" contains
28 the description of the sequence following it. Each line not
29 starting with the symbol ">" contains the sequence. Empty lines are allowed
30 and ignored when reading the input.
31 * multiple EMBL/SWISSPROT format: If the file begins with the string "ID",
32 then this file is considered to be a file in multiple EMBL format (i.e.
33 containing one or more sequences, each in EMBL format). The information
34 contained in the "ID" and "DE" lines is taken as the description of the
35 corresponding sequence. The EMBL format is identical to the SWISSPROT
36 format (w.r.t. the information we need to extract from such entries).
37 So one can also use files in multiple SWISSPROT format as input.
38 * multiple GENBANK format: If the file begins with the string "LOCUS", then
39 this file is considered to be a file in multiple GENBANK format (i.e.
40 containing one or more entries in GENBANK format). The information
41 contained in the "LOCUS" and the "DEFINITION" lines is taken as the
42 description of the corresponding sequence.
43 * plain format: If the file does not begin with the symbol ">" or the strings
44 "ID" or "LOCUS", then the file is taken verbatim. That is, the entire file
45 is considered to be the input sequence (whitespaces are not ignored).
46
47 There is no special option necessary to tell the program the sequence format.
48 It automatically detects the appropriate format, according to the rules given
49 above. If none of the above rules apply, then the program cannot recognize the
50 input format and exits with error code 1. In such a case please check you
51 input files for if they are conform with the input formats above. Another good
52 solution is to use a more versatile sequence format transformation programs
53 (e.g. *readseq*) to first generate multiple FASTA files and then feed this
54 into *mkvtree*.
55
56 Today many files containing sequence files are provided compressed by the
57 program *gzip*. To simplify the use of these files, *mkvtree* also accepts
58 gzipped input files. These files must have the ending ".gz". The gzipped
59 formatted files are gunzipped internally and then processed as any other
60 file.
61
62 ## OPTIONS
63
64 *-db* <file>::
65 Specify database files (mandatory).
66
67 *-smap* <file>::
68 Specify file containing a symbol mapping. This describes the grouping of
69 symbols. It is possible to set the environment variable MKVTREESMAPDIR
70 to the path where these files can be found.
71
72 *-dna*::
73 Input is DNA sequence.
74
75 *-protein*::
76 Input is Protein sequence.
77
78 *-indexname* <string>::
79 Specify name for index to be generated.
80
81 *-pl* <length>::
82 Specify prefix length for bucket sort.
83 Recommendation: use without argument; then a reasonable prefix length is automatically determined.
84
85 *-tis*::
86 Output transformed input sequences (tistab) to file.
87
88 *-ois*::
89 Output original input sequences (oistab) to file.
90
91 *-suf*::
92 Output suffix array (suftab) to file.
93
94 *-sti1*::
95 Output reduced inverse suffix array (sti1tab) to file.
96
97 *-bwt*::
98 Output Burrows-Wheeler Transformation (bwttab) to file.
99
100 *-bck*::
101 Output bucket boundaries (bcktab) to file.
102
103 *-skp*::
104 Output skip values (skptab) to file.
105
106 *-lcp*::
107 Output longest common prefix lengths (lcptab) to file.
108
109 *-allout*::
110 Output all index tables to files.
111
112 *-maxdepth* <len>::
113 Restrict the sorting to prefixes of the given length.
114
115 *-v*::
116 Verbose mode
117
118 *-version*::
119 Show the version of the Vmatch package.
120
121 *-help*::
122 Show help.
123
124 ## RETURNS
125
126 If an error occurs, the program exits with error code 1. Otherwise, the exit code is 0.
127
128 ## SEE ALSO
129
130 mkdna6idx(1)
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debian/mansrc/vendian.1.adoc less more
0 # vendian(1)
1
2 ## NAME
3
4 vendian - helper tool for endianness conversion
5
6 ## SYNOPSIS
7
8 *vendian* bytes filename
9
10 ## DESCRIPTION
11
12 This is used by the *vmigrate.sh* script to perform index conversion.
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debian/mansrc/vmatch.1.adoc less more
0 # vmatch(1)
1
2 ## NAME
3
4 vmatch - solve matching tasks
5
6 ## SYNOPSIS
7
8 *vmatch* [options] indexname
9
10 ## DESCRIPTION
11
12
13 The program *vmatch* allows one to solve a multitude of different matching
14 tasks over an index constructed by *mkvtree*. Each matching task is solved by
15 a combination of options specifying
16
17 * the input,
18 * the kind of matches sought,
19 * additional constraints on the matches,
20 * the direction of the matches (in case of DNA),
21 * the kind of postprocessing to be done,
22 * the output mode and output format.
23
24 Additionally, if there is more than one algorithm to solve a certain matching
25 task, *vmatch* allows to specify which algorithm is to be used.
26 *vmatch* allows to compute the following kinds of matches:
27
28 . match all substrings of the database sequences against itself. The matches
29 can be one of the following kinds:
30 .. branching tandem repeats, i.e. repeats where the two instances of the
31 repeat occur at consecutive positions
32 .. maximal repeats, i.e. pairs of maximal substrings occurring more than
33 once in the database sequences
34 .. supermaximal repeats, i.e. pairs of maximal substrings occurring more than
35 once in the database sequences, but not in any other maximal repeat
36 . match a set of query sequences (given in an extra query file) against the
37 index. The matches can be one of the following kinds:
38 .. maximal substring matches, i.e. the substrings of the query sequences
39 matching substrings of the database sequences. All matches exceeding some
40 minimum length,extended maximally to the left and to the right, are reported.
41 .. maximal unique matches, i.e. the substrings of the query sequences matching
42 substrings of the database sequences. A match is reported if it is unique in
43 the database sequences as well as in the query sequences.
44 .. complete matches, i.e. a query sequence must completely match (i.e. from the
45 first character to the last character) a substring of the database sequences.
46
47 For all these match kinds, the matches themselves can be direct or palindromic
48 (i.e. on the reverse strand, in case of DNA sequences). If required, DNA
49 sequences are translated into six reading frames and the matches are computed
50 on the protein level, and reported on the DNA level. Besides exact matches,
51 also degenerate matches with a maximal number of errors (insertions, deletions,
52 and mismatches) are supported. Moreover, degenerate matches can be derived
53 from exact matches by extending these using a greedy extension strategy. This
54 does not apply to complete matches. For all different match kinds, the matches
55 delivered by *vmatch* can be selected according to their E-value, their
56 identity value, or their match score.
57
58 In the default case, a match is reported as a formatted row of numbers,
59 containing its lengths, the positions where it occurs, the E-value, the number
60 of errors it contains, the match score, and the identity value. Optionally, an
61 alignment of the sequences that are involved in the match can be reported.
62 An important feature of *vmatch* is the capability of directly postprocessing
63 the matches found in the following ways:
64
65 . inverse output, i.e. report substrings of the database sequences or the query
66 sequences not covered by a match
67 . masking substrings of the database sequences or the query sequences covered
68 by a match
69 . clustering of a set of database sequences according to the matches found
70 between these sequences. The output of this option can be a representation of
71 the clusters, or a set of sequences each being representative for a cluster.
72 . chaining of a set of matches, i.e. finding optimal subsets of all matches
73 which do not cross
74 . clustering of matches according to the pairwise similarities on the sequences
75 involved inthe match
76 . clustering of matches according to the positions where they occur
77
78 Finally, to accommodate many more kinds of user defined post processing tasks,
79 *vmatch* provides the concept of selection functions. These provide an open
80 interface which allow arbitrary on-the-fly postprocessing of the matches
81 without output and parsing of the matches. For more details on this concept,
82 see the manual.
83
84 ## OPTIONS
85
86 *-q* <file>::
87 Specify files containing queries to be matched.
88
89 *-dnavsprot* <table>::
90 Perform six frame translation. Specify codon translation table by a number
91 in the range [1,23] except for 7, 8, 17, 18, 19 and 20; (default is 1):
92 1 Standard
93 2 Vertebrate Mitochondrial
94 3 Yeast Mitochondrial
95 4 Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
96 5 Invertebrate Mitochondrial
97 6 Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
98 9 Echinoderm Mitochondrial
99 10 Euplotid Nuclear
100 11 Bacterial
101 12 Alternative Yeast Nuclear
102 13 Ascidian Mitochondrial
103 14 Flatworm Mitochondrial
104 15 Blepharisma Macronuclear
105 16 Chlorophycean Mitochondrial
106 21 Trematode Mitochondrial
107 22 Scenedesmus Obliquus Mitochondrial
108 23 Thraustochytrium Mitochondrial
109
110 *-tandem*::
111 Compute right branching tandem repeats.
112
113 *-supermax*::
114 Compute supermaximal matches.
115
116 *-mum*::
117 Compute maximal unique matches.
118
119 *-complete*::
120 Specify that query sequences must match completely.
121
122 *-dbnomatch* <arg>::
123 Mask all database substrings containing a match; optional argument:
124 * keepleft means to not mask the left instance
125 of a match
126 * keepright means to not mask the right instance
127 of a match
128 * keepleftifsamesequence means to not mask the left instance
129 of the match if the right instance occurs
130 in the same sequence
131 * keeprightifsamesequence means to not mask the right instance
132 of the match if the left instance occurs
133 in the same sequence
134
135 *-qnomatch*::
136 Show all query substrings not containing a match.
137
138 *-dbmaskmatch* <arg>::
139 Mask all database substrings containing a match; optional argument:
140 * keepleft means to not mask the left instance
141 of a match
142 * keepright means to not mask the right instance
143 of a match
144 * keepleftifsamesequence means to not mask the left instance
145 of the match if the right instance occurs
146 in the same sequence
147 * keeprightifsamesequence means to not mask the right instance
148 of the match if the left instance occurs
149 in the same sequence
150
151 *-qmaskmatch*::
152 Mask all query substrings containing a match.
153
154 *-pp*::
155 Generic postprocessing of matches.
156
157 *-online*::
158 Run algorithms online without using the index.
159
160 *-qspeedup* <level>::
161 Specify speedup level when matching queries (0: fast, 2: faster; default is 2),
162 beware of time/space tradeoff.
163
164 *-d*::
165 Compute direct matches (default).
166
167 *-p*::
168 Compute palindromic (i.e. reverse complemented matches).
169
170 *-h* <dist>::
171 Specify the allowed hamming distance > 0. In combination with option
172 *-complete* one can switch on the percentage search mode or the best
173 search mode for the percentage search mode use an argument of the
174 form ip (where i is a positive integer). This means that up to
175 i*100/m mismatches are allowed in a match of a query of length m.
176 For the best search mode use an argument of the form ib where i is a
177 positive integer. This means that in a first phase the minimum threshold q
178 is determined such that there is still a match with q mismatches. q is in
179 the range 0 to i*100/m.
180
181 *-e* <dist>::
182 Specify the allowed edit distance > 0. In combination with option
183 *-complete* one can switch on the percentage search mode or the best
184 search mode for the percentage search mode use an argument of the
185 form ip (where i is a positive integer). This means that up to
186 i*100/m differences are allowed in a match of a query of length m.
187 For the best search mode use an argument of the form ib where i is a
188 positive integer. This means that in a first phase the minimum threshold q
189 is determined such that there is still a match with q differences. q is in
190 the range 0 to i*100/m.
191
192 *-allmax*::
193 Show all maximal matches in the order of their computation.
194
195 *-seedlength* <length>::
196 Specify the seed length.
197
198 *-hxdrop* <value>::
199 Specify the xdrop value for hamming distance extension.
200
201 *-exdrop* <value>::
202 Specify the xdrop value for edit distance extension.
203
204 *-i*::
205 Give information about number of different matches.
206
207 *-dbcluster* <args>::
208 Cluster the database sequences.
209 * first argument is percentage of shorter string
210 to be included in match,
211 * second argument is percentage of larger string
212 to be included in match,
213 * third optional argument is filenameprefix,
214 * fourth optional argument is (minclustersize, maxclustersize)
215
216 *-nonredundant*::
217 Generate file with non-redundant set of sequences; only works together
218 with option *-dbcluster*.
219
220 *-selfun* <file>::
221 Specify shared object file containing selection function.
222
223 *-l* <length>::
224 Specify that match must have the given length, optionally specify minimum
225 and maximum size of gaps between repeat instances.
226
227 *-leastscore* <score>::
228 Specify the minimum score of a match.
229
230 *-evalue* <value>::
231 Specify the maximum E-value of a match.
232
233 *-identity* <value>::
234 Specify minimum identity of match in range [1..100%].
235
236 *-sort* <mode>::
237 Sort the matches, additional argument is mode:
238 la: ascending order of length
239 ld: descending order of length
240 ia: ascending order of first position
241 id: descending order of first position
242 ja: ascending order of second position
243 jd: descending order of second position
244 ea: ascending order of Evalue
245 ed: descending order of Evalue
246 sa: ascending order of score
247 sd: descending order of score
248 ida: ascending order of identity
249 idd: descending order of identity
250
251 *-best* <n>::
252 Show the best matches (those with smallest E-values), default is best 50.
253
254 *-s*::
255 Show the alignment of matching sequences.
256
257 *-showdesc*::
258 Show sequence description of match.
259
260 *-f*::
261 Show filename where match occurs.
262
263 *-absolute*::
264 Show absolute positions.
265
266 *-nodist*::
267 Do not show distance of match.
268
269 *-noevalue*::
270 Do not show E-value of match.
271
272 *-noscore*::
273 Do not show score of match.
274
275 *-noidentity*::
276 Do not show identity of match.
277
278 *-v*::
279 Verbose mode.
280
281 *-version*::
282 Show the version of the Vmatch package.
283
284 *-help*::
285 Show basic options.
286
287 *-help+*::
288 Show all options.
289
290 ## SEE ALSO
291
292 vmatchselect(1)
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debian/mansrc/vmatchselect.1.adoc less more
0 # vmatchselect(1)
1
2 ## NAME
3
4 vmatchselect - sort and select matches
5
6 ## SYNOPSIS
7
8 *vmatchselect* [options] matchfile
9
10 ## DESCRIPTION
11
12 *vmatchselect* allows one to select interesting matches from the output of
13 vmatch as specified by user-defined criteria. It delivers matches of chosen
14 length, degeneracy or significance into further analysis routines.
15
16 *vmatchselect* removes from the input all those matches that are contained in
17 another match. To do this efficiently, the matches are sorted by their
18 position in the database sequence, and hence in the order in which the matches
19 are output, unless the user specifies otherwise. Moreover, the sequences of
20 the virtual suffix tree for which the match filewas produced can be clustered
21 according to the matches. The input for *vmatchselect* is a file produced by
22 vmatch, called a match file.
23
24 The output of *vmatchselect* goes to standard output and is sorted in
25 ascending order of the positions of the left instance of a match. Two matches
26 where the left instance occurs at the same position, are sorted in descending
27 order of their length. Two matches of the same length where the left instance
28 occurs in the same position, are sorted in ascending order of the position of
29 the right instance of the match.
30
31 *vmatchselect* provides a subset of the options of *vmatch*.
32 The main difference to *vmatch* is that *vmatchselect* gets the matches from
33 a match file, while *vmatch* computes the matches from scratch. Therefore
34 options specifying the index and/or the query sequences to be matched, as well
35 as options specifying how to match are not available in *vmatchselect*.
36 The options of *vmatchselect* have the same meaning as in the program *vmatch*.
37 Thus, for a description, see the corresponding documentation. Note that
38 *vmatchselect* also allows to use the option "-dbcluster". If *vmatchselect*
39 is called with this option, then it parses the given match file and performs
40 single linkage clustering based on the matches in this file.
41 Thus *vmatch* and *vmatchselect* allow to perform hierarchical clustering.
42 In a first step an initial set of matches with loose matching criteria is
43 computed, using *vmatch*. Then one clusters these matches by calling
44 *vmatchselect*. In a second round one applies more strict choices for the
45 matches by the using the options "-l", "-leastscore", "-evalue", or
46 "-identity", etc. This allows stepwise refinement of clusters without much
47 computational effort and no new index construction for the sequence of a
48 cluster. The output of *vmatchselect* is the same as the output of *vmatch*.
49
50 ## OPTIONS
51
52 *-dbcluster* <args>::
53 Cluster the database sequences.
54 * first argument is percentage of shorter string
55 to be included in match,
56 * second argument is percentage of larger string
57 to be included in match,
58 * third optional argument is filenameprefix,
59 * fourth optional argument is (minclustersize, maxclustersize)
60
61 *-nonredundant*::
62 Generate file with non-redundant set of sequences; only works together
63 with option *-dbcluster*.
64
65 *-selfun* <file>::
66 Specify shared object file containing selection function.
67
68 *-l* <length>::
69 Specify that match must have the given length, optionally specify minimum
70 and maximum size of gaps between repeat instances.
71
72 *-leastscore* <score>::
73 Specify the minimum score of a match.
74
75 *-evalue* <value>::
76 Specify the maximum E-value of a match.
77
78 *-identity* <value>::
79 Specify minimum identity of match in range [1..100%].
80
81 *-sort* <mode>::
82 Sort the matches, additional argument is mode:
83 la: ascending order of length
84 ld: descending order of length
85 ia: ascending order of first position
86 id: descending order of first position
87 ja: ascending order of second position
88 jd: descending order of second position
89 ea: ascending order of Evalue
90 ed: descending order of Evalue
91 sa: ascending order of score
92 sd: descending order of score
93 ida: ascending order of identity
94 idd: descending order of identity
95
96 *-best* <n>::
97 Show the best matches (those with smallest E-values), default is best 50.
98
99 *-s*::
100 Show the alignment of matching sequences.
101
102 *-showdesc*::
103 Show sequence description of match.
104
105 *-f*::
106 Show filename where match occurs.
107
108 *-absolute*::
109 Show absolute positions.
110
111 *-nodist*::
112 Do not show distance of match.
113
114 *-noevalue*::
115 Do not show E-value of match.
116
117 *-noscore*::
118 Do not show score of match.
119
120 *-noidentity*::
121 Do not show identity of match.
122
123 *-v*::
124 Verbose mode.
125
126 *-version*::
127 Show the version of the Vmatch package.
128
129 *-help*::
130 Show help.
131
132 ## SEE ALSO
133
134 vmatch(1)
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debian/mansrc/vseqinfo.1.adoc less more
0 # vseqinfo(1)
1
2 ## NAME
3
4 vseqinfo - obtain sequence information from index
5
6 ## SYNOPSIS
7
8 *vseqinfo* indexname
9
10 ## DESCRIPTION
11
12 *vseqinfo* echoes for each database sequence its length and its description.
13 The program has no options. It takes exactly one argument, namely the index
14 name. The output goes to standard output.
15
16 ## SEE ALSO
17
18 vseqselect(1)
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0 # vseqselect(1)
1
2 ## NAME
3
4 vseqselect - print selected sequences from index
5
6 ## SYNOPSIS
7
8 *vseqselect* [options] indexname
9
10 ## DESCRIPTION
11
12 The program *vseqselect* selects sequences from a given index and prints them
13 on standard output.
14
15 ## OPTIONS
16
17 *-minlength*::
18 Specify the minimal length of the sequences to be selected.
19
20 *-maxlength* <length>::
21 Specify the maximal length of the sequences to be selected.
22
23 *-randomnum* <n>::
24 Specify the number of random sequences to be selected.
25
26 *-randomlength* <length>::
27 Specify the minimal total length of the random sequences to be selected.
28
29 *-seqnum* <filename>::
30 Select the sequences with numbers given in filename.
31
32 *-version*::
33 Show the version of the Vmatch package
34
35 *-help*::
36 Show help.
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debian/mansrc/vstree2tex.1.adoc less more
0 # vstree2tex(1)
1
2 ## NAME
3
4 vstree2tex - pretty-print a virtual tree
5
6 ## SYNOPSIS
7
8 *vstree2tex* [options] indexname
9
10 ## DESCRIPTION
11
12 The program *vstree2tex* produces a representation of a virtual suffix tree
13 in LATEX format and print it to standard output. Note that *vstree2tex*
14 should only be used for very small indexes since it produces large output
15 files.
16
17 Suppose the total length of all sequences in the index is n. If the option
18 *-s* is not used, then the output size of *vstree2tex* is about 10n bytes
19 per option (plus some constant number of bytes for the header and the footer
20 of the LATEX file). If the option *-s* is used, then the size of the output
21 is proportional to n^2.
22
23 The program is mainly designed for debugging a program based on the index and
24 for educational purposes.
25
26 ## OPTIONS
27
28 *-s*::
29 Output suffixes.
30
31 *-tis*::
32 Output tistab.
33
34 *-ois*::
35 Output oistab.
36
37 *-suf*::
38 Output suftab.
39
40 *-sti1*::
41 Output small inverse suftab.
42
43 *-bwt*::
44 Output bwttab.
45
46 *-bck*::
47 Output bcktab in vertical mode.
48
49 *-bckhz*::
50 Output bcktab in horizontal mode.
51
52 *-lcp*::
53 Output lcptab.
54
55 *-skp*::
56 Output skptab.
57
58 *-cfr*::
59 Output cfrtab.
60
61 *-crf*::
62 Output crftab.
63
64 *-lsf*::
65 Output lsftab.
66
67 *-sti*::
68 Output inverse suftab.
69
70 *-cld*::
71 Output cldtab.
72
73 *-iso*::
74 Output isotab.
75
76 *-version*::
77 Show the version of the Vmatch package.
78
79 *-help*::
80 Show help.⏎
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debian/mansrc/vsubseqselect.1.adoc less more
0 # vsubseqselect(1)
1
2 ## NAME
3
4 vsubseqselect - print selected subsequences from index
5
6 ## SYNOPSIS
7
8 *vsubseqselect* [options] indexname
9
10 ## DESCRIPTION
11
12 The program *vseqselect* selects subsequences from a given index and prints
13 them on standard output, either line by line or in FASTA format. The selection
14 can either be random or according to position ranges specified by the user.
15
16 Please refer to the manual for more detailed explanations.
17
18 ## OPTIONS
19
20 *-minlength*::
21 Specify the minimal length of the substrings to be selected.
22
23 *-maxlength* <length>::
24 Specify the maximal length of the substrings to be selected.
25
26 *-snum* <n>::
27 Specify the number of random substrings to be selected.
28
29 *-range* <pos> <pos>::
30 Specify the first and last position of the substring to be selected.
31
32 *-seq* <length> <number> <pos>::
33 Specify length, number, and relative position of the substring to be selected.
34
35 *-version*::
36 Show the version of the Vmatch package
37
38 *-help*::
39 Show help.
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debian/rules less more
00 #!/usr/bin/make -f
11
2 # DH_VERBOSE := 1
2 DH_VERBOSE := 1
33 export LC_ALL=C.UTF-8
44 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
55 export PATH:=$(PATH):$(CURDIR)/src/bin
77
88 %:
99 dh $@
10
11 override_dh_auto_clean:
12 rm -rf debian/man
1013
1114 override_dh_auto_build:
1215 cd src && mklink.sh linux-gcc-64
1720 dh_auto_install
1821
1922 override_dh_installman:
20 #mkdir -p $(CURDIR)/debian/man
21 #asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man_src/*.adoc
22 #cp $(CURDIR)/debian/man_src/*.? $(CURDIR)/debian/man
23 mkdir -p $(CURDIR)/debian/man
24 asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/mansrc/*.adoc
25 mv $(CURDIR)/debian/mansrc/*.? $(CURDIR)/debian/man
2326 dh_installman --
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0 debian/man/*.1