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  1. Bug Repository
  2. BUG-622

File format issues

          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

                Sub-task - The sub-task of the issue BUG-863 Glimmer gff3 not read properly in IGB

                • Major - Major loss of function.
                • Closed

                Sub-task - The sub-task of the issue BUG-864 problem with reading gff3 file

                • Major - Major loss of function.
                • Closed

                Sub-task - The sub-task of the issue BUG-275 CHP legacy format file don't show up in table

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-8 Restore sequence to selected read (BAM)

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-27 Subsequent bam file loading causes Null Pointer Exception

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-52 The .CHP files can be loaded

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-60 Can select multiple files, but only opens one

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-66 Partial loading of BNIB files

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-76 Gff file doesn't loads correctly

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-86 Renaming a .WIG file track sustains after refresh

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-100 .wiggle files do not open (sourceforge# #3291015)

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-106 Identical file name generates a merged track.

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-177 SGR file format broken

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-187 probe sets not being displayed correctly

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-232 support SAM as well as BAM

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-250 Feature with multiple track adds track twice

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-274 Loading local .CHP file throws error on Windows

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-299 Error about loading VCF files

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-314 BigWig loading broken

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-331 NPE possibly when downloading sequence

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-341 6.7.0: drag and drop of multiple WIG files

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-426 PSLX broken on minus strand

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-523 Loading tbi indexed file from the web throws npe

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-583 Allow bed detail for saving annotations

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-593 opening *any* sequence file as a track causes each nucleotide to be overlayed with it's complement.

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-604 try loading 1000 genomes file into IGB

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-669 PSLX sequence not displayed correctly

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-690 Wig file caused multiple tracks to form for each chromosome

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-701 color Glyphs by RGB value in BED file

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-833 need to show translations in gene models from GFF that have CDS feature type

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-839 implement Cufflinks GTF parser for IGB 7.0 (as plugin?)

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-845 Handle multiple CDS in gff3

                • Major - Major loss of function.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-281 IOException when loading EST files from BioViz (Das2) server

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-315 error loading gzip file

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-434 NPE in SymLoaderTabix

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-458 Indexed GFF file does not partial load correctly

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Closed

                Bug - A problem which impairs or prevents the functions of the product. BUG-501 Handle VCF files without plug in

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Closed

                New Feature - A new feature of the product, which has yet to be developed. BUG-127 Genbank compatibility established

                • Major - Major loss of function.
                • Closed

                Task - A task that needs to be done. BUG-590 new link.psl to support Lucene searching and partial loading via tabix

                • Major - Major loss of function.
                • Closed

                Task - A task that needs to be done. BUG-305 Handle VCF files

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Closed

                Task - A task that needs to be done. BUG-307 handle Bigwig files

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Closed

                Task - A task that needs to be done. BUG-310 handle tabix files

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Closed

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                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      alyssa Alyssa Gulledge (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: