 Jeremy Goecks
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762a0becfa
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Make changes in ddea56886275 compatible with python 2.4
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2011-04-12 17:26:06 -04:00 |
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Jeremy Goecks
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c967bfa36d
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Trackster: add histogram mode to feature tracks so that user can generate coverage histogram at any level of data. Refactor overlap computation out of modules for now since it's a general purpose method used in multiple modules.
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2011-04-12 14:40:59 -04:00 |
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Kanwei Li
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7a03b066e7
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update jquery to 1.5.2, pack scripts
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2011-04-12 12:10:48 -04:00 |
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Jeremy Goecks
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2b31c9737a
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Fix bugs introduced in 03c02d86d011.
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2011-04-12 09:35:36 -04:00 |
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Jeremy Goecks
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8a44d4f5e5
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Trackster: refactor track filters out of TiledTracks and into a FiltersManager object.
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2011-04-11 14:17:35 -04:00 |
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Jeremy Goecks
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521059477e
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Enable GFF and GFF3 attributes to be written in GTF format.
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2011-04-11 12:35:23 -04:00 |
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Greg Von Kuster
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be5da0c0ef
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Fix for rating a tool in the tool shed.
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2011-04-11 10:37:14 -04:00 |
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Jeremy Goecks
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1a371da9ae
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Add tool 'Filter GTF by attribute values list.' Tool filters a GTF based on a list of attribute values; this tool is especially useful as a downstream analysis tool for filtering GTF files based on Cuffdiff outputs. Functional tests are included as well.
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2011-04-11 09:39:55 -04:00 |
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Jeremy Goecks
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9199fcab12
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Trackster: fix (a) bug that was not setting appropriate CSS class for track content divs and (b) padding issues with different track states. Also increase bottom border to better delineate tracks.
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2011-04-08 17:07:08 -04:00 |
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James Taylor
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edfb5baca9
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trackster: remove condition that sets mode to squish when less than four features in tile. mode selection must not change across tiles at the same level.
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2011-04-08 16:43:45 -04:00 |
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James Taylor
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c42268680a
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trackster: Painter class defining common interface for all painters
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2011-04-08 14:14:58 -04:00 |
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Kelly Vincent
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72c21e0067
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Removed unnecessary size check on BAM file produce in view step of sam-to-bam
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2011-04-08 12:06:28 -04:00 |
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Nate Coraor
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7125edcc0a
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Use cluster_files_directory for SGE/DRMAA instead of the hardcoded database/pbs/. Fixes issue #512 (thanks, Anonymous).
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2011-04-08 09:45:38 -04:00 |
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Nate Coraor
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8f042a795b
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Use JobWrapper.get_job() since it's there.
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2011-04-08 09:37:33 -04:00 |
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Jeremy Goecks
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3171c8b024
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Fix hyperlinks in Cuffcompare and Cuffdiff documentation.
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2011-04-07 16:28:56 -04:00 |
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Daniel Blankenberg
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daf645f53a
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Additional fix for typo propagated from manual_builds, which was updated in 5350:cd2aff5b117c.
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2011-04-07 08:39:07 -04:00 |
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Kelly Vincent
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8d6ec35964
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Added BWA for SOLiD to tool_conf.xml.main
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2011-04-06 16:28:33 -04:00 |
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Nate Coraor
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0e33ca6acc
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Disable eagerloading of a job's datasets. This results in more queries but does away with a join that was returning a far bigger result than it should've.
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2011-04-06 12:44:58 -04:00 |
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Kanwei Li
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0bc3b0aff0
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Delete unused BLAST tests
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2011-04-06 12:40:20 -04:00 |
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Kanwei Li
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af3f4a2ff9
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More BLAST tests
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2011-04-06 12:38:00 -04:00 |
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Kelly Vincent
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d969f29c01
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Corrected typo in manual build name
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2011-04-06 10:16:30 -04:00 |
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Jeremy Goecks
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60ac2204e8
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Trackster: ensure that reads are drawn in squish and pack modes even when view area is large by setting a minimum width of 1px.
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2011-04-05 17:59:43 -04:00 |
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Jeremy Goecks
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dc36e0beed
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Merge.
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2011-04-05 14:16:26 -04:00 |
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Jeremy Goecks
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125dc5896f
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Merge.
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2011-04-05 14:14:32 -04:00 |
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Ross Lazarus
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d6945af461
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reverted unintended changes to tool_conf.xml.main
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2011-04-05 14:14:08 -04:00 |
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Jeremy Goecks
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5f5f659402
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Trackster: mode is not reduced if in auto mode.
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2011-04-05 14:12:39 -04:00 |
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Ross Lazarus
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70c8eccee0
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change to weblogo test jpg comparison and code cleanups to rgCaCo
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2011-04-05 14:07:10 -04:00 |
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Ross Lazarus
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a22e453676
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merge
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2011-04-05 13:57:14 -04:00 |
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Nate Coraor
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4d4f1763d8
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Added clustalw and weblogo tools to Main tool_conf. Thanks Ross.
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2011-04-05 12:08:42 -04:00 |
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Jeremy Goecks
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6416659211
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Refactor and enhance trackster visual analytics: (a) move all visual analytics code into Tool class for encapsulation; (b) put tool outputs in appropriate history when user is rerunning his own tool; (c) enable users not logged in to run tools; (d) use tool HTML to display inputs rather than sliders.
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2011-04-05 11:51:48 -04:00 |
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James Taylor
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63582942cd
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trackster: draw lines to indicate when line tracks overflow the visible region
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2011-04-04 23:27:25 -04:00 |
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James Taylor
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f21278e49c
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trackster: fix read track drawing offsets for all modes
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2011-04-04 13:40:09 -04:00 |
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Kanwei Li
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b5d8d577ca
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BLAST test changes
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2011-04-04 12:55:33 -04:00 |
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James Taylor
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5a6dec9a4a
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trackster: some fixes for read tracks
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2011-04-03 12:47:39 -04:00 |
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James Taylor
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7631db87e6
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trackster: typo
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2011-04-03 12:40:28 -04:00 |
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James Taylor
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51ca021998
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trackster: tabs. why won't this editor respect my authority?
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2011-04-02 23:13:38 -04:00 |
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James Taylor
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f9db75311d
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trackster: fix bug with fetching same data many times by putting deferred in data cache immediately, still problematic because many deferred callbacks are queued up and the tile is drawn multiple times, debug statement demonstrates this, needs more refactoring to get it right
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2011-04-02 23:12:02 -04:00 |
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James Taylor
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474ee073bb
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trackster: disabling subsetting in data manager, breaks line tracks
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2011-04-02 18:30:13 -04:00 |
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James Taylor
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2f233b446b
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trackster: drawing labels on left at start of chrom works again, tweaks to feature track padding
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2011-04-02 17:35:27 -04:00 |
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Jeremy Goecks
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09d2657696
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Gracefully handle parsing errors in GFFReader and accurately compute raw size of GFF features.
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2011-04-02 16:43:02 -04:00 |
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James Taylor
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d89596f1a8
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trackster: everything now contained in three distinct modules using CommonJS exports/require style, more fixing coupling and global variables
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2011-04-02 16:02:30 -04:00 |
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James Taylor
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1b5bc59367
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Use extend everywhere instead of $.extend
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2011-04-02 14:46:42 -04:00 |
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James Taylor
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e41c38fedf
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trackster: draw intron/exon structure in dense mode, also restore border top for all tracks
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2011-04-02 14:36:52 -04:00 |
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James Taylor
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3f3af03da3
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trackster: draw inverted fishbones for genes with UTRs but no introns (one block with meaningful thick region)
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2011-04-02 13:34:08 -04:00 |
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James Taylor
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9b7ef47d98
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trackster: fixing tabs again
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2011-04-02 13:02:43 -04:00 |
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James Taylor
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c41719902d
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trackster: thick region should not be drawn when thick_stat == thick_end (this indicates no thick region). Non-coding genes draw correctly now
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2011-04-02 13:01:25 -04:00 |
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James Taylor
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2eb08910af
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trackster: encapsulate tracks in a closure to ensure global variables are not leaking, eliminated many global variables and moved others to the painters (where they should become configurable). Should have no globals that are shared between Tracks and Painters. Also, some drawing tweaks: thicker dense display, cleaner axis line for line tracks, when in auto mode, the actual mode is displayed in parens
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2011-04-02 12:20:22 -04:00 |
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James Taylor
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f0063baf57
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trackster: making extensions to CanvasRenderingContext regular functions, extending built-ins is verboten, breaks encapsulation
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2011-04-02 10:05:24 -04:00 |
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Daniel Blankenberg
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4432911038
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Better handling of errors on rerun when grouping constructs have been added or removed.
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2011-04-01 18:10:47 -04:00 |
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Jeremy Goecks
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11ec423833
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Do not use from_work_dir in Tophat because it causes set_metadata to fail on BAM output when run on a cluster.
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2011-04-01 11:36:55 -04:00 |
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