Camelia, the Perl 6 bug

IRC log for #bioperl, 2013-03-08

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All times shown according to UTC.

Time Nick Message
00:39 flu joined #bioperl
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12:54 virushunter deafferret: howdy
14:49 bot48 joined #bioperl
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17:45 deafferret virushunter: hi!
17:50 virushunter deafferret: hello...how are you
17:57 virushunter <off to lunch>
17:57 deafferret virushunter: good, thanks! enjoy lunch! :)
17:58 deafferret brb coffee
18:39 GOW joined #bioperl
18:44 GOW Hi Everyone, I have a question about using Bio::DB::Sam. I am able to use Bio::DB::Sam->new(-bam ....) etc to read a bam file and parse individual alignements. But, I dont know how to write it back as an "sam formated" line or 'bam"
18:44 GOW can any one help me?
18:45 GOW I could write it if I read the alignments with Bio::DB::Bam->open('new.bam', 'w')
18:46 GOW not when i read it with Bio::DB::Sam->new()
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19:09 scottcain GOW: Let me start with I don't really know.
19:10 scottcain GOW: what do you want to do?  (at a higher level than "write into a BAM file")
19:25 scottcain GOW: also, since the author of Bio::Samtools doesn't hang out here, I'd suggest an email to the mailing list.
19:33 GOW Thanks Scott. I will email the list. But, in brief, I read a bam file, try to use XM, XS, AS tags to do some filtering (per mismatch, alignment scores etc), Than write only the records that passed this quality check.
19:34 GOW I am having trouble converting the alignmnet object (from Bio::DB::Sam method) into a writeable string
20:15 virushunter deafferret: recently Francisco Ossandon submitted a pull request  https://github.com/bioperl/bioperl-live/pull/52
20:16 virushunter deafferret: all the tests for blast.t pass successfully, so it there anything else to do but perform....
20:16 virushunter the git pull https://github.com/fjossandon/bioperl-live master
20:16 virushunter and git push origin master?
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20:29 deafferret virushunter: nope. if the code looks good to you and you're satisfied that all applicable tests are >= to how they previously were -- then click that "Merge" button!  (Or do it manually in git if you prefer.)
20:30 deafferret virushunter: what's the state of the automated test harness thing? /me looks
20:31 deafferret huh, where'd that thing go? I thought it was prominent on https://github.com/bioperl/bioperl-live at one point?
20:32 virushunter deafferret: what, the test harness thing?
20:32 deafferret ya, there was some automated test runner hooked to the repo at one point
20:32 virushunter deafferret: travis?
20:34 virushunter deafferret: https://github.com/bioperl/bioperl-live/pull/52 says travis build passed
20:34 deafferret ya! ... oh it's in the pull thing? cool. pass is good :)
20:35 virushunter deafferret: yeah, I'm satisfied with the code fix and the tests that he wrote. But this doesn't mean that I completely understand what he did.
20:35 deafferret #shipit  :)
20:35 virushunter deafferret: i'm going to click that tempting merge button :)
20:35 deafferret if it looks clean, not insane, and tests >= they were then I say go for it
20:36 virushunter deafferret: shipped ;)
20:36 github [bioperl-live] pcantalupo pushed 4 new commits to master: https://github.com/bioperl/bioperl-liv​e/compare/e0e6cf811b47...d5c7e755dcb3
20:36 github bioperl-live/master dc5696b unknown: Fixed no-hit blast bug and faulty regexs, added tests
20:36 github bioperl-live/master f3c0f98 Francisco J. Ossandon: Revert "Fixed no-hit blast bug and faulty regexs, added tests"...
20:36 github bioperl-live/master d02ef18 Francisco J. Ossandon: Fix for Bug #3251, plus fixed a couple of regular expressions. Also added tests....
20:36 deafferret Travis green light is nice too, but the red travis' i've seen were false alarms
20:36 virushunter good to know
20:36 virushunter I've been helping Francisco get started on github
20:36 virushunter sort of how you helped me out
20:36 deafferret info from me should be categorized under "rumors" not "knowledge" :)
20:37 virushunter lol
20:37 deafferret woot! pay it forward!
20:37 virushunter yeah feels good to empower other people
20:37 deafferret virushunter: ya, so when he does a couple and feels good about it you can make him collab
20:37 virushunter I don't think I can do that, can I/
20:37 deafferret virushunter: then we break both your kneecaps when he screws up :)
20:37 virushunter ?
20:38 deafferret bioperl development is a pyramid scheme :)
20:38 virushunter :(
20:38 deafferret um... lemme look
20:39 deafferret virushunter: can you get here or does it not allow you?  https://github.com/organiz​ations/bioperl/teams/4111
20:39 deafferret that's the push/pull "team", apparently
20:39 virushunter yes
20:39 deafferret wow. 19 bioperl/ repos
20:39 deafferret the monolith is slowly succumbing to modules :)
20:39 virushunter yeah and the list is growing as modules are split out
20:39 deafferret woot!
20:39 * deafferret high-fives virushunter
20:40 virushunter what is 'mode/#bioperl ....'?
20:40 deafferret you're an IRC operator now
20:40 deafferret congrats!
20:40 virushunter sweet
20:40 deafferret so now type /kick deafferret
20:41 virushunter sounds good but don't know what it means
20:41 deafferret was kicked by virushunter: deafferret
20:41 virushunter ah ha
20:41 deafferret joined #bioperl
20:41 deafferret :)
20:42 virushunter jay, so what is your job?
20:42 deafferret programmer for http://www.iinteractive.com
20:42 virushunter been there long?
20:43 deafferret um, almost 2 years i think
20:43 virushunter how do I find out more about that IRC operator thingy
20:44 deafferret um, http://freenode.net/using_the_network.shtml
20:45 virushunter cool thanks...well I best be getting back to my real job
20:46 deafferret oh wow, 2 years on Apr 1
20:46 deafferret ... I was an April Fool's joke, apparently :)
20:46 virushunter congrats
20:46 virushunter lol
20:46 virushunter i had my 20th anniversary in feb
20:46 deafferret virushunter: toodles! see you around :)
20:46 virushunter later
20:46 deafferret virushunter: oh, wow. ya, I left my 11-year corporate gig ~3 years back
20:46 deafferret telecommuting++
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