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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/docs/differences.README @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 -- RUNTIME COMPARISON --
2 Compute mum candidates of length >= 100.
3 Result is identical for both programs.
4
5 mummer3: mummer2:
6
7 Ecoli K12/
8 Ecoli 0157: 14 sec/66 MB 17 sec/133 MB
9
10 Ecoli 0157/
11 Ecoli K12: 14 sec/77 MB 17 sec/155 MB
12
13 S cerevisae/
14 S pombe 42 sec/172 MB 50 sec/348 MB
15
16 S pombe/
17 S cerevisae 41 sec/176 MB 52 sec/358 MB
18
19
20
21 -- CORRECTNESS COMPARISON --
22 Consider the two files
23
24 > N25
25 NNNNNNNNNNNNNNNNNNNNNNNNN
26
27 and nn.query
28
29 > n18
30 nnnnnnnnnnnnnnnnnn
31
32 ------------------ First example:---------------
33 mummer3 -l 5 Data/nn.query Data/nn.subject
34 > N25
35 1 1 18
36 1 2 18
37 1 3 18
38 1 4 18
39 1 5 18
40 1 6 18
41 1 7 18
42 1 8 18
43
44 mummer2 -l 5 Data/nn.query Data/nn.subject
45 > N25
46 1 1 18
47
48 I think the result of mummer3 is correct, since the
49 string n18 occurs exactly once in n18. It occurs 8
50 times in N25. hence 8 MUM-candidates are reported.
51
52 ---- second example -----
53
54 mummer3.x -l 5 Data/nn.subject Data/nn.query
55 > n18
56
57 Bigmum.sh -l 5 Data/nn.subject Data/nn.query
58 > n18
59 New string is suffix of reference string
60 8 1 18
61
62 Here n18 occurs several times in the N25, hence it is
63 not a MUM-candidates and so nothing is to be reported.
64 Thus the result of mummer3 is correct.