Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/docs/differences.README @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 -- RUNTIME COMPARISON -- |
| jpayne@69 | 2 Compute mum candidates of length >= 100. |
| jpayne@69 | 3 Result is identical for both programs. |
| jpayne@69 | 4 |
| jpayne@69 | 5 mummer3: mummer2: |
| jpayne@69 | 6 |
| jpayne@69 | 7 Ecoli K12/ |
| jpayne@69 | 8 Ecoli 0157: 14 sec/66 MB 17 sec/133 MB |
| jpayne@69 | 9 |
| jpayne@69 | 10 Ecoli 0157/ |
| jpayne@69 | 11 Ecoli K12: 14 sec/77 MB 17 sec/155 MB |
| jpayne@69 | 12 |
| jpayne@69 | 13 S cerevisae/ |
| jpayne@69 | 14 S pombe 42 sec/172 MB 50 sec/348 MB |
| jpayne@69 | 15 |
| jpayne@69 | 16 S pombe/ |
| jpayne@69 | 17 S cerevisae 41 sec/176 MB 52 sec/358 MB |
| jpayne@69 | 18 |
| jpayne@69 | 19 |
| jpayne@69 | 20 |
| jpayne@69 | 21 -- CORRECTNESS COMPARISON -- |
| jpayne@69 | 22 Consider the two files |
| jpayne@69 | 23 |
| jpayne@69 | 24 > N25 |
| jpayne@69 | 25 NNNNNNNNNNNNNNNNNNNNNNNNN |
| jpayne@69 | 26 |
| jpayne@69 | 27 and nn.query |
| jpayne@69 | 28 |
| jpayne@69 | 29 > n18 |
| jpayne@69 | 30 nnnnnnnnnnnnnnnnnn |
| jpayne@69 | 31 |
| jpayne@69 | 32 ------------------ First example:--------------- |
| jpayne@69 | 33 mummer3 -l 5 Data/nn.query Data/nn.subject |
| jpayne@69 | 34 > N25 |
| jpayne@69 | 35 1 1 18 |
| jpayne@69 | 36 1 2 18 |
| jpayne@69 | 37 1 3 18 |
| jpayne@69 | 38 1 4 18 |
| jpayne@69 | 39 1 5 18 |
| jpayne@69 | 40 1 6 18 |
| jpayne@69 | 41 1 7 18 |
| jpayne@69 | 42 1 8 18 |
| jpayne@69 | 43 |
| jpayne@69 | 44 mummer2 -l 5 Data/nn.query Data/nn.subject |
| jpayne@69 | 45 > N25 |
| jpayne@69 | 46 1 1 18 |
| jpayne@69 | 47 |
| jpayne@69 | 48 I think the result of mummer3 is correct, since the |
| jpayne@69 | 49 string n18 occurs exactly once in n18. It occurs 8 |
| jpayne@69 | 50 times in N25. hence 8 MUM-candidates are reported. |
| jpayne@69 | 51 |
| jpayne@69 | 52 ---- second example ----- |
| jpayne@69 | 53 |
| jpayne@69 | 54 mummer3.x -l 5 Data/nn.subject Data/nn.query |
| jpayne@69 | 55 > n18 |
| jpayne@69 | 56 |
| jpayne@69 | 57 Bigmum.sh -l 5 Data/nn.subject Data/nn.query |
| jpayne@69 | 58 > n18 |
| jpayne@69 | 59 New string is suffix of reference string |
| jpayne@69 | 60 8 1 18 |
| jpayne@69 | 61 |
| jpayne@69 | 62 Here n18 occurs several times in the N25, hence it is |
| jpayne@69 | 63 not a MUM-candidates and so nothing is to be reported. |
| jpayne@69 | 64 Thus the result of mummer3 is correct. |