| Time |
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| 00:33 |
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| 02:47 |
|
CIA-57 |
bioperl-live: Robert Buels master * ref979d2 / Bio/Root/RootI.pm : improved _rearrange performance by 30% - http://bit.ly/hWOAd4 |
| 03:19 |
|
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| 03:20 |
|
rbuels |
dukeleto: ^^^^ |
| 03:20 |
|
rbuels |
(_rearrange is called many many times by 90% of bioperl in tight loops) |
| 03:20 |
|
dukeleto |
rbuels: ooh, shiny |
| 03:20 |
|
dukeleto |
rbuels: where is your benchmark script? |
| 03:21 |
|
dukeleto |
rbuels: you should commit it as a benchmark test, so we can see if people make it slow again |
| 03:21 |
|
rbuels |
dukeleto: my benchmark was me running nytprof a few times |
| 03:21 |
|
rbuels |
dukeleto: you have a good benchmark-test module to recommend? |
| 03:22 |
|
dukeleto |
rbuels: Tool::Bench |
| 03:22 |
|
dukeleto |
rbuels: buy anything will do |
| 03:23 |
|
dukeleto |
rbuels: https://github.com/notbenh/tool_bench |
| 03:23 |
|
dukeleto |
rbuels: not sure if it has hit CPAN yet |
| 03:23 |
|
rbuels |
dukeleto: how could i normalize the benchmark for people's machines in such a way that it would show if somebody made it slower? |
| 03:23 |
|
rbuels |
dukeleto: have a reference implementation? |
| 03:23 |
|
rbuels |
dukeleto: (in the test)? |
| 03:25 |
|
dukeleto |
rbuels: i am just saying to have the script, it doesn't necessary need to pass or fail |
| 03:25 |
|
dukeleto |
rbuels: but having something where people can say "this took X seconds on this commit by Y seconds on that commit" is valuable |
| 03:26 |
|
dukeleto |
rbuels: perhaps a benchmarks/ directory is needed |
| 03:26 |
|
dukeleto |
rbuels: something akin to https://github.com/parrot/parr[…]amples/benchmarks |
| 03:28 |
|
dukeleto |
rbuels: anyway, nice work |
| 03:28 |
|
dukeleto |
rbuels: have you thought of writing _rearrange in XS ? ::ducks:: |
| 03:32 |
|
* rbuels |
rolls his eyes |
| 03:51 |
|
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| 04:19 |
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| 04:22 |
|
CIA-57 |
bioperl-live: Robert Buels master * r108312d / Bio/SeqFeature/Generic.pm : improved Bio::SeqFeature::Generic::has_tag performance by about 30% - http://bit.ly/gED7QH |
| 04:22 |
|
CIA-57 |
bioperl-live: Robert Buels master * r68a5215 / Bio/Location/Atomic.pm : fix big performance regression in which _load_module was getting called every time(!) a new Bio::Location::Atomic (and subclasses) was created - http://bit.ly/gfsDjq |
| 04:26 |
|
rbuels |
Devel::NYTProf is wonderful. (as if it needed more praise) |
| 04:27 |
|
rbuels |
sheenams: welcome to the matrix. |
| 04:27 |
|
* rbuels |
chuckles |
| 04:27 |
|
sheenams |
haha....don't make me choose a pill color. |
| 04:28 |
|
rbuels |
sheenams: oh no, by starting your irc client you have already swallowed the red one. |
| 04:28 |
|
sheenams |
oh ok. well at least i didn't have to google which one I wanted. I don't remember the movie that well |
| 04:29 |
|
rbuels |
sheenams: i'm actually just now headed out, but we'll skype tomorrow |
| 04:29 |
|
sheenams |
ok. i'm working on getting skype to function in ubuntu. the mike volume is incredibly low and I can't seem to change it. |
| 04:29 |
|
rbuels |
sheenams: i don't know if pyrimidine will be there or not (pyrimidine == chris ) |
| 04:30 |
|
sheenams |
well I'm sure you'll be able to answer a bunch of my questions anyways. |
| 04:30 |
|
sheenams |
do you know dan bolser? |
| 04:30 |
|
rbuels |
sheenams: sure of course. |
| 04:30 |
|
rbuels |
(i know dan) |
| 04:30 |
|
rbuels |
sheenams: he's in this channel now, dbolser |
| 04:30 |
|
sheenams |
i tried to message him about gsoc but he didn't get back to me. have an email address I can send it to? |
| 04:31 |
|
rbuels |
sheenams: did he say something odd to you about "talk to duke"? |
| 04:32 |
|
sheenams |
no. i mentioned that duke told me to talk to him... |
| 04:32 |
|
rbuels |
everything is become clear to me now. |
| 04:32 |
|
rbuels |
dukeleto: ^^^^^ |
| 04:34 |
|
rbuels |
sheenams: in more recent ubuntu, you might need to use pavucontrol to adjust skype's volume levels |
| 04:34 |
|
rbuels |
sheenams: or the system volume control |
| 04:34 |
|
rbuels |
sheenams: especially if you are using an external headset |
| 04:35 |
|
sheenams |
i'll work on that. no external headset so I have to rely on the built in mike (i know, i lose nerd points for that) |
| 04:39 |
|
* rbuels |
finds skype really annoying |
| 04:40 |
|
sheenams |
agreed. even with input volume at 150% its really quiet. |
| 04:40 |
|
sheenams |
windows 7 it is for skype (and onenote) |
| 04:42 |
|
sheenams |
it works if i yell at it.... |
| 04:42 |
|
rbuels |
sheenams: we could use google voice if you can get that working better |
| 04:42 |
|
rbuels |
sheenams: that has a linux client too |
| 04:42 |
|
sheenams |
thats what i use for most chats |
| 04:48 |
|
sheenams |
google voice/video chat is good to go in ubuntu. |
| 04:52 |
|
* rbuels |
works on it |
| 05:02 |
|
rbuels |
sheenams: ok, i think i have it working on my end also |
| 05:03 |
|
* rbuels |
goes to bed |
| 05:03 |
|
sheenams |
night |
| 05:03 |
|
CIA-57 |
bioperl-live: Robert Buels master * re40cfe6 / (3 files in 3 dirs): add test for leading whitespace before exonerate query, fix to work with old exonerate format (you should run the tests hyphaltip!) - http://bit.ly/eNZSxO |
| 05:53 |
|
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| 07:18 |
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| 08:26 |
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| 09:42 |
|
dbolser |
hi sheenams... IRC is like email, except when you log off, I've no frickin idea how to contact you again... |
| 09:44 |
|
dbolser |
anyone got an email for sheenams? I'll lurk while the world turns. |
| 09:45 |
|
dbolser |
rbuels: good work with the performance boosts |
| 10:12 |
|
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| 12:16 |
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| 13:07 |
|
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| 13:07 |
|
rbuels |
had a nice night last night with Devel::NYTProf |
| 13:29 |
|
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| 13:41 |
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| 13:45 |
|
pyrimidine |
rbuels: wondered whether you started profiling. Devel::NYTProf is nice! |
| 13:46 |
|
rbuels |
pyrimidine: yeah, i had nytprof out cause i was playing with the refactored ace.pm |
| 13:46 |
|
rbuels |
(rewritten, really) |
| 13:46 |
|
rbuels |
so much better |
| 13:46 |
|
|
driley_ is now known as driley |
| 13:47 |
|
pyrimidine |
yeah, there are defin. parts that could use a good profiler, others that just need to be simpler in design |
| 13:47 |
|
pyrimidine |
***cough***Locations***cough*** |
| 13:47 |
|
rbuels |
yeah. |
| 13:48 |
|
rbuels |
pyrimidine: well, you saw that Locations thing i did |
| 13:48 |
|
pyrimidine |
rbuels: yep |
| 13:48 |
|
rbuels |
pyrimidine: that cut 5 sec off of a 33-second runtime |
| 13:48 |
|
pyrimidine |
rbuels: did you see my branch commit? |
| 13:49 |
|
* rbuels |
looks |
| 13:49 |
|
pyrimidine |
https://github.com/bioperl/bio[…]/cached_locations |
| 13:49 |
|
rbuels |
iiiinteresting |
| 13:50 |
|
pyrimidine |
the problem is, any parsers need to reset the cache |
| 13:50 |
|
pyrimidine |
but there is a decent speedup for large seqs |
| 13:51 |
|
rbuels |
pyrimidine: what parsers use from_str |
| 13:51 |
|
dbolser |
ace++ |
| 13:52 |
|
dbolser |
For feature intersections I'm using Set::IntRange |
| 13:52 |
|
dbolser |
quite fast |
| 13:53 |
|
pyrimidine |
rbuels: There is a Bio::Factory::FTLocationFactory in Bio::SeqIO; I think GenBank and EMBL use that for generating locations, and Bio::SeqIO::FTHelper does other bits of gruntwork |
| 13:53 |
|
pyrimidine |
(though FTHelper should just go away, it's extraneous) |
| 13:53 |
|
rbuels |
pyrimidine: seems like the caching should be something that's handled by the parsers that are creating locations |
| 13:54 |
|
rbuels |
(creating them willy-nilly) |
| 13:54 |
|
alxsi |
can someone explain me this line please? my @cds = grep { $_->primary_tag eq 'CDS' } $seq->get_SeqFeatures; |
| 13:54 |
|
pyrimidine |
rbuels: thought about that. but then each parser is implementing an independent caching system |
| 13:54 |
|
rbuels |
alxsi: do you know perl? |
| 13:54 |
|
pyrimidine |
s/is/would be/ |
| 13:54 |
|
rbuels |
pyrimidine: yeah it is, but caching under the covers is a Bad Idea |
| 13:55 |
|
rbuels |
pyrimidine: you could make a LocationCacher i suppose |
| 13:55 |
|
rbuels |
pyrimidine: so they only need to be poked a *little* to add the caching |
| 13:55 |
|
pyrimidine |
rbuels: yeah, that's probably a better idea |
| 13:55 |
|
rbuels |
but caching magically inside the location stuff ... |
| 13:55 |
|
rbuels |
that'll lead to trouble |
| 13:56 |
|
pyrimidine |
rbuels: or, something that wraps the LocationFactory and specifically implements caching |
| 13:56 |
|
rbuels |
that would work too |
| 13:56 |
|
pyrimidine |
rbuels: the caching is settable, and off by default |
| 13:57 |
|
rbuels |
pyrimidine: make sure the cache doesn't start getting huge |
| 13:57 |
|
pyrimidine |
rbuels: though I like the wrapper idea more (decouples the caching behavior from the everything else) |
| 13:58 |
|
pyrimidine |
rbuels: right; the parser would be responsible for resetting the cache |
| 13:58 |
|
pyrimidine |
dbolser: have you tried any of the SQLite RTree stuff? |
| 13:58 |
|
dbolser |
alxsi: rbuels means you should lookup grep |
| 13:58 |
|
dbolser |
pyrimidine: no, is it positional indexing? |
| 13:58 |
|
pyrimidine |
dbolser: spatial indexing |
| 13:59 |
|
dbolser |
oh right |
| 13:59 |
|
pyrimidine |
I just added a patch that made it into CPAN in the latest DBD::SQLite release |
| 13:59 |
|
pyrimidine |
*dev release |
| 13:59 |
|
alxsi |
yes I looked it up, but I don't really understand it's use |
| 13:59 |
|
pyrimidine |
http://search.cpan.org/~adamk/DBD-SQLite-1.32_02/ |
| 14:00 |
|
rbuels |
alxsi: it filters a list, giving the results as another list |
| 14:00 |
|
rbuels |
alxsi: just like the shell command 'grep' filters a stream |
| 14:01 |
|
dbolser |
alxsi: my @values_equal_to_1 = grep{ $_ == 1 } @values; |
| 14:01 |
|
pyrimidine |
my @filtered_sfs = grep {$_->has_tag('CDS') } $seq->get_SeqFeatures; |
| 14:01 |
|
alxsi |
so this gets all the values from @values that == 1? |
| 14:02 |
|
dbolser |
pyrimidine: using Set::IntRange within feature sets is more general than using SQLite though... |
| 14:02 |
|
dbolser |
alxsi: yup, no tvery usefull, but yeah |
| 14:02 |
|
dbolser |
you get a list of 1s at best... |
| 14:02 |
|
dbolser |
but in the bp example, you get all objects where the tag is CDS |
| 14:03 |
|
dbolser |
primary_tag that is |
| 14:03 |
|
dbolser |
l8r |
| 14:03 |
|
alxsi |
ok yes i got it thanks for clearing that up |
| 14:04 |
|
pyrimidine |
dbolser: does it work directly across specifically identified ranges (like chromosomes)? For instance, would it differentiate 1..10 on chr1 vs 1..10 on chrX? |
| 14:05 |
|
pyrimidine |
I know that you can do a prelim test on that, but DBD::SQLite's RTree can do that directly, with a bit of magic |
| 14:06 |
|
pyrimidine |
dbolser: just curious on that bit; I'm working on a generic non-bioperl backend that abstracts that away, so a pure perl solution would be nice |
| 14:07 |
|
pyrimidine |
(mysql and Pg also implement RTree, though Pg has it in a separate module) |
| 14:10 |
|
dbolser |
pyrimidine: no, Set::IntRange is very crude |
| 14:10 |
|
dbolser |
low level |
| 14:10 |
|
dbolser |
in fact I'm not even sure if it would be efficient on chromosome scale feature sets |
| 14:11 |
|
pyrimidine |
dbolser: that's okay. Just so you know, there are a few other pure perl-based modules that do the same thing, just not sure of their performance |
| 14:11 |
|
dbolser |
right |
| 14:11 |
|
pyrimidine |
dbolser: apparently, DBD::SQLite is used by a number of devs who work with SNPS, can handle millions of features |
| 14:12 |
|
pyrimidine |
and the RTree implementation is supposed to scale better than binning and other schemes (acc. to Jim Kent's BigWig paper, which uses this) |
| 14:16 |
|
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| 14:37 |
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| 14:37 |
|
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| 14:38 |
|
andrei_ |
hey guys |
| 14:39 |
|
andrei_ |
I was just wandering if when you extract a CDS sequence from .gbk file, and in the gbk is said that the sequence is complement, does bioperl reverse it when it extracts it? |
| 14:40 |
|
andrei_ |
CDS complement(26161..27204) |
| 14:41 |
|
andrei_ |
this is how it looks in the benbank file |
| 14:41 |
|
pyrimidine |
andrei_: if it is a feature, and you call '$sf->seq', it returns the sequence based on the location, so yes |
| 14:41 |
|
andrei_ |
ok thanks |
| 14:43 |
|
pyrimidine |
andrei_: just a small gotcha: if you call $sf->seq and the location is split (e.g. feature has multiple locations with a join, like exons) then you should call spliced_seq() |
| 15:01 |
|
andrei_ |
yes I know, but if the l0ocation is not split? can I still call sliced_seq()? |
| 15:06 |
|
pyrimidine |
andrei_: yes, it doesn't hurt, but it is a bit slower for obvious reasons |
| 15:36 |
|
CIA-57 |
bioperl-live: Chris Fields master * r97074c7 / MANIFEST : update manifest - http://bit.ly/fvttkc |
| 15:39 |
|
pyrimidine |
oh, ffs. The remote database changed back for the Map.t tests, failing again. grrr.... |
| 15:45 |
|
pyrimidine |
rbuels: bioperl seems .... snappier |
| 15:45 |
|
pyrimidine |
:) |
| 15:46 |
|
* pyrimidine |
using the update meme : http://www.google.com/search?s[…]seems+snappier%22 |
| 15:50 |
|
* rbuels |
chuckles |
| 16:04 |
|
dbolser |
pyrimidine: thanks for that tip, I may be involved in a big snp project next year |
| 16:09 |
|
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| 16:10 |
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| 16:11 |
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| 16:33 |
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| 17:25 |
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| 17:25 |
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| 17:32 |
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| 17:46 |
|
pyrimidine |
posts on Redmine and using OpenID for BioPerl wiki: http://news.open-bio.org/news/ |
| 17:46 |
|
* pyrimidine |
goes back to his regularly scheduled hacking |
| 17:49 |
|
pyrimidine |
dukeleto: apparently redmine doesn't like the quotes in your name |
| 17:50 |
|
pyrimidine |
dukeleto: the other email notification error was a bug with the bugzilla transition to redmine that I fixed |
| 17:51 |
|
pyrimidine |
dukeleto: fixed the quoting thing as well, so you should be able to login |
| 18:01 |
|
rbuels |
sheenams: is your google voice thing ringing? |
| 18:20 |
|
dukeleto |
pyrimidine: yes, my quotes find lots of bugs in various places :) |
| 18:20 |
|
dukeleto |
pyrimidine: thanks for fixing stuff |
| 18:21 |
|
pyrimidine |
dukeleto: np |
| 18:21 |
|
dukeleto |
pyrimidine: the redmine instance should really use SSL, or else we will tempt the Firesheep gods |
| 18:23 |
|
pyrimidine |
dukeleto: I can check into that with Chris D, not sure what the apache setup is on that EC2 instance |
| 18:24 |
|
pyrimidine |
I think it is configured for SSL though |
| 18:29 |
|
pyrimidine |
ah, no it isn't. will check with chris d then to see what is going on |
| 18:35 |
|
dukeleto |
pyrimidine: thanks! we don't want anybody to hack our gibsons |
| 18:38 |
|
pyrimidine |
dukeleto: posted to the powers that be. should get a response soonish |
| 18:46 |
|
* rbuels |
just finished talking to sheenams about the bioperl reorg |
| 18:46 |
|
rbuels |
heh, whatever happens, she'll learn a lot! i'm giving her a little pre-project to extract a module from the SGN codebase and CPAN it |
| 18:46 |
|
dukeleto |
rbuels: good lord, you are mean |
| 18:47 |
|
rbuels |
depends on what module I pick :-) |
| 18:47 |
|
sheenams |
dukeleto: don't egg him on! i'm a noob over here... |
| 18:49 |
|
sheenams |
rbuels: just remember, you're the one I'll be asking to help me when i get stuck. |
| 18:49 |
|
* rbuels |
chuckles |
| 18:49 |
|
dukeleto |
sheenams: indeed. he is a glutton for punishment |
| 18:49 |
|
rbuels |
sheenams: you've got pyrimidine too, don't forget |
| 18:49 |
|
rbuels |
don't let that guy off too easy |
| 18:49 |
|
* pyrimidine |
ducks |
| 18:50 |
|
rbuels |
he's going to be benefitting a lot from a reorg |
| 18:50 |
|
pyrimidine |
everyone will benefit from a reorg |
| 18:50 |
|
|
mzgrideng left #bioperl |
| 18:54 |
|
sheenams |
i'll make sure my email questions go to both of you. and maybe duke too for the fun of it. |
| 19:08 |
|
dukeleto |
sheenams: oh boy! |
| 19:11 |
|
pyrimidine |
:) |
| 19:37 |
|
|
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| 19:37 |
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| 19:55 |
|
rbuels |
pyrimidine: i've got some de novo assemblies of RNA-seq data to get some unigene-like things. |
| 19:55 |
|
rbuels |
pyrimidine: for petunia, which has no genome right now. |
| 19:55 |
|
rbuels |
pyrimidine: was done with MIRA, I only have a .ace file. |
| 19:56 |
|
rbuels |
pyrimidine: need to put this ace in some kind of database, or index it or something. what would you recommend? |
| 19:56 |
|
rbuels |
pyrimidine: SAM/BAM seems to be for reference-based stuff, which this isn't ... |
| 19:57 |
|
pyrimidine |
I think Florent recently hacked Bio::Assembly to store data in a Bio::DB::SeqFeature::Store |
| 19:57 |
|
rbuels |
pyrimidine: yep i see that |
| 19:57 |
|
rbuels |
pyrimidine: each Bio::Assembly::Contig has a seqfeature::store in-memory |
| 19:57 |
|
pyrimidine |
ick |
| 19:57 |
|
rbuels |
pyrimidine: well, it works OK ... |
| 19:57 |
|
rbuels |
pretty fast too |
| 19:58 |
|
pyrimidine |
sure, but that sort of defeats the purpose of Bio::DB::SeqFeature::Store |
| 19:58 |
|
pyrimidine |
which is capable of storing lots of (uniquely-named) seqs and features |
| 19:58 |
|
rbuels |
pyrimidine: but anyway, i want to make a page like this, but for an assembled bunch of RNA-seq: http://solgenomics.net/search/[…]ne_id=SGN-U444444 |
| 19:58 |
|
rbuels |
pyrimidine: particularly the "mRNA member sequences" part |
| 19:59 |
|
rbuels |
(collapsed by default) |
| 19:59 |
|
rbuels |
though i would probably only display the coverage part of that graphic by default |
| 19:59 |
|
rbuels |
pyrimidine: so, i would have a detail page like this for each de-novo-assembled transcript sequences |
| 20:00 |
|
pyrimidine |
rbuels: yeah, that sounds about right |
| 20:00 |
|
rbuels |
pyrimidine: so i need to look up each contig's assembly someplace ... so i'm trying to figure out where to put it |
| 20:00 |
|
rbuels |
not in chado. |
| 20:00 |
|
rbuels |
could index the .ace file .... |
| 20:00 |
|
rbuels |
could maybe put it in a Bio::DB::SeqFeature::Store |
| 20:01 |
|
rbuels |
or could i actually use a BAM for this? |
| 20:01 |
|
pyrimidine |
I think the Store |
| 20:01 |
|
pyrimidine |
BAM would also work, yes |
| 20:01 |
|
pyrimidine |
each contig would be a reference sequence |
| 20:01 |
|
pyrimidine |
that the reads map to |
| 20:02 |
|
rbuels |
i'm thinking about integrating LookSeq at some point |
| 20:02 |
|
rbuels |
seen it? |
| 20:02 |
|
pyrimidine |
not yet |
| 20:02 |
|
rbuels |
s'pretty nice |
| 20:02 |
|
rbuels |
pyrimidine: http://www.sanger.ac.uk/cgi-bi[…]/lookseq/index.pl |
| 20:02 |
|
rbuels |
lot better than gbrowse for looking at an assembly |
| 20:03 |
|
rbuels |
pyrimidine: http://www.sanger.ac.uk/resour[…]software/lookseq/ |
| 20:03 |
|
rbuels |
(and also http://sourceforge.net/projects/lookseq/) |
| 20:04 |
|
pyrimidine |
it's pretty nice! |
| 20:05 |
|
rbuels |
sure is. i was kind of shocked to find it today |
| 20:05 |
|
rbuels |
it runs off of some kind of custom sqlite db |
| 20:06 |
|
pyrimidine |
yeah, that's what I'm seeing as well |
| 20:06 |
|
rbuels |
and of course they couldn't be bothered to ping anybody else about it, like GMOD or OBF, apparently |
| 20:06 |
|
pyrimidine |
heh |
| 20:06 |
|
pyrimidine |
not unusual, though |
| 20:07 |
|
pyrimidine |
lots of reworked wheels, even within Sanger |
| 20:08 |
|
rbuels |
well, i'm not aware of any web-based assembly viewer that's this sophisticated |
| 20:08 |
|
rbuels |
are you? |
| 20:08 |
|
pyrimidine |
not at this leve; |
| 20:08 |
|
pyrimidine |
*level |
| 20:09 |
|
pyrimidine |
good to see that it's still developed, bad to see that it has a bus factor = 1 |
| 20:09 |
|
rbuels |
hehe |
| 20:10 |
|
pyrimidine |
sorry, 2 |
| 20:13 |
|
pyrimidine |
they are replicating some of the samtools efforts with bcftools |
| 20:13 |
|
pyrimidine |
at least that |
| 20:13 |
|
pyrimidine |
's how it looks |
| 20:13 |
|
pyrimidine |
http://samtools.sourceforge.net/mpileup.shtml |
| 20:15 |
|
rbuels |
even more amazing, from the samtools man page: "Heng Li from the Sanger Institute wrote the C version of samtools." |
| 20:15 |
|
rbuels |
lol |
| 20:15 |
|
rbuels |
maybe they don't actually overlap ... |
| 20:15 |
|
* rbuels |
doesn't know much about this |
| 20:15 |
|
pyrimidine |
dunno |
| 20:16 |
|
pyrimidine |
though it does store variant call information, which is what bcftools is geared towards |
| 20:21 |
|
CIA-57 |
bioperl-live: Chris Fields master * r54fb1e7 / t/Map/Map.t : |
| 20:21 |
|
CIA-57 |
bioperl-live: Revert "volatile data broke test". Remote database changed data back. |
| 20:21 |
|
CIA-57 |
bioperl-live: This reverts commit 4b69c5e4333990821def4a3a5db2b8645da71b6c. - http://bit.ly/hozENl |
| 20:21 |
|
rbuels |
o_O |
| 20:21 |
|
pyrimidine |
rbuels: Ensembl issues |
| 20:26 |
|
CIA-57 |
bioperl-live: Chris Fields release-1-6-2 * ra037bef / : Merge branch 'release-1-6-2' of github.com:bioperl/bioperl-live into release-1-6-2 (+9 more commits...) - http://bit.ly/dTyGKb |
| 20:28 |
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| 20:30 |
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sl33v3_ is now known as sl33v3 |
| 20:35 |
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| 21:02 |
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* rbuels |
is getting pretty close to the point of writing Bio::Index::Ace |
| 21:17 |
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| 23:25 |
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deafferret |
Ventura Pet Detective |
| 23:29 |
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| 23:50 |
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dbolser |
rbuels: BAM is quite nippy, And is the emerging standard for short read submission at SRA |
| 23:51 |
|
dbolser |
night |
| 23:52 |
|
dbolser |
(I'm off skiing tomorrow, so if I don't see you guys AgAin, good luck with this whole 'bio-perl'thing |
