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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 | kortsch: you're a loose cannon! | |
| 05:55 | 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 | http://ec2-174-129-70-67.compu[…]azonaws.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 | oh baby AMI ID: ami-2675974f | |
| 09:13 | tarbo2_ joined #bioperl | |
| 13:11 | brandi joined #bioperl | |
| 13:12 | brandi left #bioperl | |
| 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 |
| 16:13 | brandi joined #bioperl | |
| 16:22 | brandi left #bioperl | |
| 16:42 | brandi joined #bioperl | |
| 17:37 | brandi joined #bioperl | |
| 18:58 | * deafferret | feeds the phant breakfast |
| 19:05 | brandi left #bioperl | |
| 19:25 | ptl joined #bioperl | |
| 20:53 | brunov joined #bioperl | |
| 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 |
| 21:49 | alireza joined #bioperl | |
| 21:51 | alireza left #bioperl | |
| 22:02 | ptl_ joined #bioperl | |
| 22:29 | ptl joined #bioperl | |
| 22:52 | brunov joined #bioperl |
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