Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-12-17

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All times shown according to UTC.

Time Nick Message
00:11 balin joined #bioperl
00:27 fualo joined #bioperl
01:50 brunov joined #bioperl
02:24 brandi joined #bioperl
03:36 driveby_bot joined #bioperl
03:36 driveby_bot /home/svn-repositories/bioperl: r16472 (maj) : lots of fixes and addns/ can create databases and masks
03:40 driveby_bot joined #bioperl
03:40 driveby_bot /home/svn-repositories/bioperl: r16473 (maj) : fixes to CommandExts
03:40 * deafferret clutches chest, collapses
04:08 driveby_bot joined #bioperl
04:08 driveby_bot /home/svn-repositories/bioperl: r16474 (kortsch) : Transfered current state of Bowtie.pm in my bioperl-run repo.
04:08 driveby_bot joined #bioperl
04:08 driveby_bot /home/svn-repositories/bioperl: r16475 (kortsch) : Mainly doc and copyright notification changes - one bug fix in Bowtie.t
04:09 * deafferret clutches chest, collapses
04:09 deafferret phant: go ... on ... without me  !
04:09 driveby_bot joined #bioperl
04:09 driveby_bot /home/svn-repositories/bioperl: r16476 (kortsch) : Added test suite data - permission granted by Ben Langmead.
04:10 driveby_bot joined #bioperl
04:10 driveby_bot /home/svn-repositories/bioperl: r16477 (kortsch) : Most tests defined - need to add confirming output of a run matches expectations.
04:11 driveby_bot joined #bioperl
04:11 driveby_bot /home/svn-repositories/bioperl: r16478 (kortsch) : Minor change to file spec definition for paired.
04:11 driveby_bot joined #bioperl
04:11 driveby_bot /home/svn-repositories/bioperl: r16479 (kortsch) : Bug fix in inline sequence test.
04:11 driveby_bot joined #bioperl
04:11 driveby_bot /home/svn-repositories/bioperl: r16480 (kortsch) : Minor change to Bowtie test
04:11 driveby_bot joined #bioperl
04:11 driveby_bot /home/svn-repositories/bioperl: r16481 (kortsch) : Minor change to Bowtie test
04:11 driveby_bot joined #bioperl
04:11 driveby_bot /home/svn-repositories/bioperl: r16482 (kortsch) : Reorganisation of some tests to allow for sub command param testing properly
04:11 driveby_bot joined #bioperl
04:11 driveby_bot /home/svn-repositories/bioperl: r16483 (kortsch) : This fucking 'S' keeps coming back!
04:11 driveby_bot joined #bioperl
04:11 driveby_bot /home/svn-repositories/bioperl: r16484 (kortsch) : Remove # from like tests.
04:12 driveby_bot joined #bioperl
04:12 driveby_bot /home/svn-repositories/bioperl: r16485 (kortsch) : Various doc changes.
04:12 driveby_bot joined #bioperl
04:12 driveby_bot /home/svn-repositories/bioperl: r16486 (kortsch) : More doc changes.
04:12 driveby_bot joined #bioperl
04:12 driveby_bot /home/svn-repositories/bioperl: r16487 (kortsch) : Index file name var no point to the index, not an absent space.
04:12 driveby_bot joined #bioperl
04:12 driveby_bot /home/svn-repositories/bioperl: r16488 (kortsch) : Fix close bug in _run
04:12 driveby_bot joined #bioperl
04:12 driveby_bot /home/svn-repositories/bioperl: r16489 (kortsch) : Filespec determination in cases for single and paired bowties.
04:12 driveby_bot joined #bioperl
04:12 driveby_bot /home/svn-repositories/bioperl: r16490 (kortsch) : Nicer version for crossbow.
04:12 driveby_bot joined #bioperl
04:12 driveby_bot /home/svn-repositories/bioperl: r16491 (kortsch) : Drop program name off options list - not used by bowtie
04:13 driveby_bot joined #bioperl
04:13 driveby_bot /home/svn-repositories/bioperl: r16492 (kortsch) : Dealing with residual undefs in @files.
04:13 driveby_bot joined #bioperl
04:13 driveby_bot /home/svn-repositories/bioperl: r16493 (kortsch) : Fixed bug - calling run, rather than run_bowtie.
04:13 driveby_bot joined #bioperl
04:13 driveby_bot /home/svn-repositories/bioperl: r16494 (kortsch) : run now appropriately sets named filespec params, which have been simplified in Config.pm (seq1 to seq). Changes to Bowtie.t to take this into account.
04:13 driveby_bot joined #bioperl
04:13 driveby_bot /home/svn-repositories/bioperl: r16495 (kortsch) : Clean up unused comments from Mark.
04:13 driveby_bot joined #bioperl
04:13 driveby_bot /home/svn-repositories/bioperl: r16496 (kortsch) : Force into SAM output from bowtie.
04:13 driveby_bot joined #bioperl
04:13 driveby_bot /home/svn-repositories/bioperl: r16497 (kortsch) : Remove redundant line left from Maq.
04:14 driveby_bot joined #bioperl
04:14 driveby_bot /home/svn-repositories/bioperl: r16498 (kortsch) : SAM param requirements - rest to 0 explicitly.
04:14 driveby_bot joined #bioperl
04:14 driveby_bot /home/svn-repositories/bioperl: r16499 (kortsch) : Trying to sort out output file passing.
04:14 driveby_bot joined #bioperl
04:14 driveby_bot /home/svn-repositories/bioperl: r16500 (kortsch) : Test for _run - output checked and counted.
04:14 driveby_bot joined #bioperl
04:14 driveby_bot /home/svn-repositories/bioperl: r16501 (kortsch) : Added code to convert the SAM output of bowtie to BAM so that the B:A:I:s can cope with it.
04:14 driveby_bot joined #bioperl
04:14 driveby_bot /home/svn-repositories/bioperl: r16502 (kortsch) : Defined version as a separate program.
04:14 driveby_bot joined #bioperl
04:14 driveby_bot /home/svn-repositories/bioperl: r16503 (kortsch) : Fixed calls to Samtools sort.
04:15 driveby_bot joined #bioperl
04:15 driveby_bot /home/svn-repositories/bioperl: r16504 (kortsch) : Remove default to SAM output.
04:15 driveby_bot joined #bioperl
04:15 driveby_bot /home/svn-repositories/bioperl: r16505 (kortsch) : Version now registered, SAM format exclusive setting now presaged.
04:15 driveby_bot joined #bioperl
04:15 driveby_bot /home/svn-repositories/bioperl: r16506 (kortsch) : Fit version call before file requirement checks.
04:15 driveby_bot joined #bioperl
04:15 driveby_bot /home/svn-repositories/bioperl: r16507 (kortsch) : Running version program insists version switch is set.
04:15 driveby_bot joined #bioperl
04:15 driveby_bot /home/svn-repositories/bioperl: r16508 (kortsch) : Removed version return function - may re-add. In with_version fork.
04:15 driveby_bot joined #bioperl
04:15 driveby_bot /home/svn-repositories/bioperl: r16509 (kortsch) : Nicer line count code for output test.
04:15 driveby_bot joined #bioperl
04:15 driveby_bot /home/svn-repositories/bioperl: r16510 (kortsch) : Test numbers now correct.
04:15 driveby_bot joined #bioperl
04:15 driveby_bot /home/svn-repositories/bioperl: r16511 (kortsch) : Parameter following - prevent incompatible switches/params, ensure requirements.
04:16 driveby_bot joined #bioperl
04:16 driveby_bot /home/svn-repositories/bioperl: r16512 (kortsch) : Tried to build on AssmeblyBase method - no good. This uses the AssemblyBase code.
04:16 driveby_bot joined #bioperl
04:16 driveby_bot /home/svn-repositories/bioperl: r16513 (kortsch) : Documentation largely up-to-date.
05:15 driveby_bot joined #bioperl
05:15 driveby_bot /home/svn-repositories/bioperl: r16514 (kortsch) : Try sort out inline sequence passing.
05:15 driveby_bot joined #bioperl
05:15 driveby_bot /home/svn-repositories/bioperl: r16515 (kortsch) : Inline sequences now handled appropriately.
05:17 deafferret damn. drive-by genocide
05:17 deafferret kortsch: you're a loose cannon!
05:55 deafferret oooo ... custom bioperl Amazon EC2 images?  fortinbras-public/bioperl-max-0.1.2.manifest.xml
07:04 rbuels deafferret: go to bed
07:05 deafferret rbuels: NO U
07:05 deafferret http://ec2-174-129-70-67.co​mpute-1.amazonaws.com:3000/
07:05 rbuels NUH UH U R A ASS
07:06 * rbuels titters girlishly
07:06 deafferret now if only I could get an EBS Root Device so I can make my own AMI
07:13 deafferret oh baby  AMI ID: ami-2675974f
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13:38 brunov joined #bioperl
13:40 driveby_bot joined #bioperl
13:40 driveby_bot /home/svn-repositories/bioperl: r16516 (dave_messina) : file-level metadata parsing of the opening <seqXML> tag now done when the seqIO object is created (in _initialize), rather than waiting till we get to next_seq. Added tests for this.
16:13 driveby_bot joined #bioperl
16:13 driveby_bot /home/svn-repositories/bioperl: r16517 (maj) : masking works pretty well; start db make and mask integration
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18:58 * deafferret feeds the phant breakfast
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20:56 driveby_bot joined #bioperl
20:56 driveby_bot /home/svn-repositories/bioperl: r16518 (maj) : ok,looks like its actually masking on request
21:05 * deafferret dons his mask, per request
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