[BUG-622] File format issues - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Blocker
Resolution: Fixed
Labels:
None

Description

This bug deals with various file format issues. Please ensure that you have Test File Repository access (either drop box or downloaded) before beginning this series of bug tests.

Attachments

Issue Links

relates to

BUG-863 Glimmer gff3 not read properly in IGB

Closed

BUG-864 problem with reading gff3 file

Closed

BUG-275 CHP legacy format file don't show up in table

Closed

BUG-8 Restore sequence to selected read (BAM)

Closed

BUG-27 Subsequent bam file loading causes Null Pointer Exception

Closed

BUG-52 The .CHP files can be loaded

Closed

BUG-60 Can select multiple files, but only opens one

Closed

BUG-66 Partial loading of BNIB files

Closed

BUG-76 Gff file doesn't loads correctly

Closed

BUG-86 Renaming a .WIG file track sustains after refresh

Closed

BUG-100 .wiggle files do not open (sourceforge# #3291015)

Closed

BUG-106 Identical file name generates a merged track.

Closed

BUG-177 SGR file format broken

Closed

BUG-187 probe sets not being displayed correctly

Closed

BUG-232 support SAM as well as BAM

Closed

BUG-250 Feature with multiple track adds track twice

Closed

BUG-274 Loading local .CHP file throws error on Windows

Closed

BUG-299 Error about loading VCF files

Closed

BUG-314 BigWig loading broken

Closed

BUG-331 NPE possibly when downloading sequence

Closed

BUG-341 6.7.0: drag and drop of multiple WIG files

Closed

BUG-426 PSLX broken on minus strand

Closed

BUG-523 Loading tbi indexed file from the web throws npe

Closed

BUG-583 Allow bed detail for saving annotations

Closed

BUG-593 opening *any* sequence file as a track causes each nucleotide to be overlayed with it's complement.

Closed

BUG-604 try loading 1000 genomes file into IGB

Closed

BUG-669 PSLX sequence not displayed correctly

Closed

BUG-690 Wig file caused multiple tracks to form for each chromosome

Closed

BUG-701 color Glyphs by RGB value in BED file

Closed

BUG-833 need to show translations in gene models from GFF that have CDS feature type

Closed

BUG-839 implement Cufflinks GTF parser for IGB 7.0 (as plugin?)

Closed

BUG-845 Handle multiple CDS in gff3

Closed

BUG-281 IOException when loading EST files from BioViz (Das2) server

Closed

BUG-315 error loading gzip file

Closed

BUG-434 NPE in SymLoaderTabix

Closed

BUG-458 Indexed GFF file does not partial load correctly

Closed

BUG-501 Handle VCF files without plug in

Closed

BUG-127 Genbank compatibility established

Closed

BUG-590 new link.psl to support Lucene searching and partial loading via tabix

Closed

BUG-305 Handle VCF files

Closed

BUG-307 handle Bigwig files

Closed

BUG-310 handle tabix files

Closed

Show 37 more links (37 relates to)

Activity

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Alyssa Gulledge (Inactive) created issue - 15/Nov/12 9:53 AM

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Field	Original Value	New Value
Link		This issue relates to ~~BUG-27~~ [ ~~BUG-27~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-52~~ [ ~~BUG-52~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-53~~ [ ~~BUG-53~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-60~~ [ ~~BUG-60~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-66~~ [ ~~BUG-66~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-76~~ [ ~~BUG-76~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-81~~ [ ~~BUG-81~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-86~~ [ ~~BUG-86~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-100~~ [ ~~BUG-100~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-106~~ [ ~~BUG-106~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-111~~ [ ~~BUG-111~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-162~~ [ ~~BUG-162~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-177~~ [ ~~BUG-177~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-274~~ [ ~~BUG-274~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-275~~ [ ~~BUG-275~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-299~~ [ ~~BUG-299~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-305~~ [ ~~BUG-305~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-307~~ [ ~~BUG-307~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:01 AM

Assignee

Ann Loraine [ aloraine ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:03 AM

Link

This issue relates to ~~BUG-281~~ [ ~~BUG-281~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:16 AM

Link

This issue relates to ~~BUG-310~~ [ ~~BUG-310~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:16 AM

Link

This issue relates to ~~BUG-315~~ [ ~~BUG-315~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:16 AM

Link

This issue relates to ~~BUG-341~~ [ ~~BUG-341~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:16 AM

Link

This issue relates to ~~BUG-374~~ [ ~~BUG-374~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:16 AM

Link

This issue relates to ~~BUG-458~~ [ ~~BUG-458~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:16 AM

Link

This issue relates to ~~BUG-523~~ [ ~~BUG-523~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:16 AM

Link

This issue relates to ~~BUG-593~~ [ ~~BUG-593~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:16 AM

Link

This issue relates to ~~BUG-604~~ [ ~~BUG-604~~ ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:17 AM

Link

This issue relates to ~~BUG-81~~ [ ~~BUG-81~~ ]

Alyssa Gulledge (Inactive) made changes - 20/Nov/12 9:01 AM

Issue Type

Bug [ 1 ]

Task [ 3 ]

Alyssa Gulledge (Inactive) made changes - 26/Nov/12 9:08 AM

Assignee

Alyssa Gulledge [ alyssa ]

Richard Linchangco [ richard ]

Alyssa Gulledge (Inactive) made changes - 28/Nov/12 5:59 AM

Link

This issue relates to ~~BUG-111~~ [ ~~BUG-111~~ ]

Alyssa Gulledge (Inactive) made changes - 28/Nov/12 6:10 AM

Link

This issue relates to ~~OLD-46~~ [ ~~OLD-46~~ ]

Alyssa Gulledge (Inactive) made changes - 28/Nov/12 10:53 AM

Link

This issue relates to ~~BUG-374~~ [ ~~BUG-374~~ ]

Richard Linchangco (Inactive) made changes - 05/Dec/12 7:23 AM

Status	Open [ 1 ]	Resolved [ 5 ]
Assignee	Richard Linchangco [ richard ]	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 06/Dec/12 7:42 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 06/Dec/12 7:46 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 06/Dec/12 7:48 AM

Status	Reopened [ 4 ]	Closed [ 6 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 10/Dec/12 8:27 AM

Link

This issue relates to ~~OLD-44~~ [ ~~OLD-44~~ ]

Alyssa Gulledge (Inactive) made changes - 10/Dec/12 8:27 AM

Link

This issue relates to ~~BUG-434~~ [ ~~BUG-434~~ ]

Alyssa Gulledge (Inactive) made changes - 10/Dec/12 8:27 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 11/Dec/12 8:06 AM

Link

This issue relates to ~~BUG-669~~ [ ~~BUG-669~~ ]

Alyssa Gulledge (Inactive) made changes - 11/Dec/12 8:37 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 11/Dec/12 8:37 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 12/Dec/12 5:23 AM

Link

This issue relates to ~~BUG-232~~ [ ~~BUG-232~~ ]

Alyssa Gulledge (Inactive) made changes - 12/Dec/12 5:25 AM

Link

This issue relates to ~~BUG-127~~ [ ~~BUG-127~~ ]

Alyssa Gulledge (Inactive) made changes - 12/Dec/12 5:32 AM

Link

This issue relates to ~~BUG-314~~ [ ~~BUG-314~~ ]

Alyssa Gulledge (Inactive) made changes - 18/Dec/12 6:39 AM

Link

This issue relates to ~~BUG-331~~ [ ~~BUG-331~~ ]

Alyssa Gulledge (Inactive) made changes - 18/Dec/12 6:54 AM

Link

This issue relates to ~~BUG-187~~ [ ~~BUG-187~~ ]

Alyssa Gulledge (Inactive) made changes - 18/Dec/12 7:16 AM

Link

This issue relates to ~~BUG-8~~ [ ~~BUG-8~~ ]

Alyssa Gulledge (Inactive) made changes - 18/Dec/12 7:26 AM

Link

This issue relates to ~~BUG-250~~ [ ~~BUG-250~~ ]

Alyssa Gulledge (Inactive) made changes - 19/Dec/12 4:17 AM

Link

This issue relates to ~~BUG-426~~ [ ~~BUG-426~~ ]

Alyssa Gulledge (Inactive) made changes - 19/Dec/12 8:53 AM

Link

This issue relates to ~~BUG-583~~ [ ~~BUG-583~~ ]

Alyssa Gulledge (Inactive) made changes - 20/Dec/12 11:13 AM

Link

This issue relates to ~~BUG-501~~ [ ~~BUG-501~~ ]

Alyssa Gulledge (Inactive) made changes - 20/Dec/12 11:47 AM

Link

This issue relates to ~~BUG-590~~ [ ~~BUG-590~~ ]

Alyssa Gulledge (Inactive) made changes - 20/Dec/12 11:48 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Richard Linchangco [ richard ]

Alyssa Gulledge (Inactive) made changes - 20/Dec/12 11:52 AM

Status	Reopened [ 4 ]	Closed [ 6 ]
Assignee	Richard Linchangco [ richard ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 02/Jan/13 9:11 AM

Link

This issue relates to ~~BUG-690~~ [ ~~BUG-690~~ ]

Alyssa Gulledge (Inactive) made changes - 07/Jan/13 8:40 AM

Link

This issue relates to ~~BUG-701~~ [ ~~BUG-701~~ ]

Alyssa Gulledge (Inactive) made changes - 02/Oct/13 5:57 AM

Link

This issue relates to ~~BUG-833~~ [ ~~BUG-833~~ ]

Alyssa Gulledge (Inactive) made changes - 02/Oct/13 5:58 AM

Link

This issue relates to ~~BUG-845~~ [ ~~BUG-845~~ ]

Alyssa Gulledge (Inactive) made changes - 02/Oct/13 5:58 AM

Link

This issue relates to ~~BUG-863~~ [ ~~BUG-863~~ ]

Alyssa Gulledge (Inactive) made changes - 02/Oct/13 5:58 AM

Link

This issue relates to ~~BUG-864~~ [ ~~BUG-864~~ ]

Alyssa Gulledge (Inactive) made changes - 02/Oct/13 5:58 AM

Link

This issue relates to ~~BUG-839~~ [ ~~BUG-839~~ ]

People

Assignee:

Unassigned

Reporter:

Alyssa Gulledge (Inactive)

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Dates

Created:

15/Nov/12 9:53 AM

Updated:

02/Oct/13 5:58 AM

Resolved:

20/Dec/12 11:52 AM