Timeline for Counting k-mers
Current License: CC BY-SA 3.0
47 events
| when toggle format | what | by | license | comment | |
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| Feb 7, 2023 at 4:28 | history | edited | The Fifth Marshal |
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| Mar 2, 2015 at 22:46 | vote | accept | CommunityBot | moved from User.Id=9206 by developer User.Id=3572 | |
| S Feb 12, 2015 at 11:02 | history | bounty ended | CommunityBot | ||
| S Feb 12, 2015 at 11:02 | history | notice removed | user9206 | ||
| Feb 7, 2015 at 16:09 | answer | added | user16991 | timeline score: 6 | |
| Feb 6, 2015 at 21:42 | history | edited | user9206 | CC BY-SA 3.0 |
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| Feb 6, 2015 at 17:17 | comment | added | FUZxxl | @Lembik Would you mind rating my solution? | |
| Feb 6, 2015 at 2:07 | answer | added | FUZxxl | timeline score: 8 | |
| Feb 4, 2015 at 21:04 | history | edited | user9206 | CC BY-SA 3.0 |
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| S Feb 4, 2015 at 18:21 | history | bounty started | CommunityBot | ||
| S Feb 4, 2015 at 18:21 | history | notice added | user9206 | Draw attention | |
| Feb 3, 2015 at 18:06 | history | edited | user9206 | CC BY-SA 3.0 |
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| Feb 3, 2015 at 6:05 | answer | added | Keith Randall | timeline score: 8 | |
| Feb 2, 2015 at 23:36 | comment | added | FUZxxl | @Lembik I improved my solution. It's not the new strategy I am thinking about though. | |
| Feb 2, 2015 at 21:27 | comment | added | FUZxxl | @Lembik I won't tell you because I'm afraid someone implements the approach and beats me. I can tell you later, when it's done. | |
| Feb 2, 2015 at 21:24 | comment | added | FUZxxl | @Lembik I won't tell you. I'm currently in the process of altering the solution so it gives output earlies (but is slower overall). It take 9 minutes to preprocess the data on my machine. | |
| Feb 2, 2015 at 21:13 | comment | added | user9206 | @FUZxxl What is it? I am very interested. | |
| Feb 2, 2015 at 20:47 | comment | added | FUZxxl | I found a wonderful method to compute the indices for all k in very brief time, but the preprocessing takes so long -.- | |
| Feb 2, 2015 at 20:02 | comment | added | user9206 | @randomra I updated the question. Please let me know if it helps. | |
| Feb 2, 2015 at 19:59 | history | edited | user9206 | CC BY-SA 3.0 |
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| Feb 2, 2015 at 19:12 | history | edited | user9206 | CC BY-SA 3.0 |
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| Feb 2, 2015 at 19:07 | history | edited | user9206 | CC BY-SA 3.0 |
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| Feb 2, 2015 at 19:02 | history | edited | user9206 | CC BY-SA 3.0 |
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| Feb 2, 2015 at 18:59 | comment | added | user9206 | @PeterTaylor Yes to reading from a ready-decompressed file. No to stripping the newlines beforehand. Handling newlines should be part of the code that is timed. | |
| Feb 2, 2015 at 18:58 | comment | added | user9206 | @KeithRandall You are right it is all out by one currently. | |
| Feb 2, 2015 at 18:37 | comment | added | Peter Taylor | When you say "You can decompress the input before starting the timing.": a) Does that include a licence to read the input from a ready-decompressed file? b) Does it include a licence to strip the newlines from that prepared file? | |
| Feb 2, 2015 at 18:33 | comment | added | FUZxxl | Huch? Are you sure? Let me remove that… | |
| Feb 2, 2015 at 18:30 | comment | added | Keith Randall | @FUZxxl: ah, I need to remove \n first. You have a bug also though, the +1 after ftello() allows one zero byte to sneak in at the end. | |
| Feb 2, 2015 at 18:17 | history | edited | FUZxxl | CC BY-SA 3.0 |
add two more lines of sample output.
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| Feb 2, 2015 at 18:06 | comment | added | FUZxxl | @KeithRandall The first few solutions I get are 15, 93, 521, 2924, 15715, 71331, 265862, 890896, and 2482913. I'm not sure if they are correct, but OP thinks so. | |
| Feb 2, 2015 at 18:02 | comment | added | Keith Randall | I get 110 for k==2. Could you double-check the correct result? | |
| Feb 2, 2015 at 18:01 | comment | added | randomra | Can we use the special properties of the given file to improve the effectiveness of our program on the test? (While producing correct output for any input.) | |
| Feb 2, 2015 at 17:37 | history | edited | user9206 | CC BY-SA 3.0 |
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| Feb 2, 2015 at 17:26 | comment | added | user9206 | @FUZxxl You can assume a file called chr2.fa as input. If you want it on stdin you will need to pipe it. The order of the output matters. It should be for k = 1,2,3,4,5,6,7,... in that order. The output is one number per line. | |
| Feb 2, 2015 at 15:32 | answer | added | FUZxxl | timeline score: 2 | |
| Feb 2, 2015 at 13:52 | comment | added | FUZxxl | Are we allowed to put trailing spaces into the output? | |
| Feb 2, 2015 at 13:41 | comment | added | FUZxxl | Does the order matter in which we output the entries in one line? With what character are they separated? | |
| Feb 2, 2015 at 13:37 | comment | added | FUZxxl |
Is there any restriction on how input has to be provided? Can we assume input comes from stdin and is attached to a file?
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| Feb 2, 2015 at 13:35 | comment | added | FUZxxl | Is a solution required to abort itself after one minute or are you going to do this? | |
| Feb 2, 2015 at 11:42 | history | tweeted | twitter.com/#!/StackCodeGolf/status/562214400158101504 | ||
| Feb 2, 2015 at 11:24 | comment | added | user9206 | @FUZxxl Well... please feel free to submit it as an answer :) Remember I cut it off at 2GB of RAM. | |
| Feb 2, 2015 at 11:22 | comment | added | FUZxxl | Well, for 2 it returns in about 5 seconds, for 3 it take 3.2 GB of RAM and takes about a minute. I didn't try what it would do for four. Let me try... | |
| Feb 2, 2015 at 11:19 | history | edited | user9206 | CC BY-SA 3.0 |
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| Feb 2, 2015 at 11:11 | comment | added | user9206 | @FUZxxl Well... how large a k does it give you in one minute and much RAM does it use? | |
| Feb 2, 2015 at 11:10 | comment | added | FUZxxl |
In J, a naïve solution would simply be `[:~.]` but guess that won't cut it.
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| Feb 2, 2015 at 10:18 | history | edited | user9206 | CC BY-SA 3.0 |
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| Feb 2, 2015 at 9:46 | history | asked | user9206 | CC BY-SA 3.0 |