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The software company Atlassian granted to the Flux Capacitor project an Open Source License for their JIRA tracking system. Please feel free to employ this system to report any issue (e.g., bugs, requests for enhancement, etc.) concerning the Flux Simulator. In order to create issues or to monitor the development progress on any existing issue, you need to create an account that at the same time also allows to post and comment on discussions in this wiki. Before reporting new issues, browse the list below or search JIRA for the existence of identical or closely related topics. Refer to the Wiki Markup syntax for formatting options.

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Flux Capacitor Issues (20 issues)

T Key Status Resolution Updated P Summary
Story BARNA-383 Resolved Fixed Oct 09, 2015 Major unknown macro-latex inline errors all over the place in flux simulator documentation
Epic BARNA-381 Resolved Fixed Oct 09, 2015 Major Unable to reach the downloads for any flux package
Story BARNA-376 Resolved Fixed Oct 09, 2015 Major Some boolean parameters need to be renamed to have the default value as false
Improvement BARNA-375 Resolved Fixed Oct 09, 2015 Minor Add MIN_OBS parameter to allow quantifications for loci with spurious reads
Bug BARNA-374 Resolved Fixed Oct 09, 2015 Major Capacitor overquantify a transcript in a locus when using only sam primary alignments
Bug BARNA-373 Resolved Fixed Oct 09, 2015 Major Capacitor does not deconvolute locus when using only sam primary alignments
Improvement BARNA-372 Reopened Unresolved Oct 09, 2015 Major Output annotation mapped reads
Improvement BARNA-367 Resolved Fixed Oct 09, 2015 Major Simplification of delta values
Improvement BARNA-366 Resolved Fixed Oct 09, 2015 Major Joint deconvolution of paired-end reads
Bug BARNA-365 Open Unresolved Oct 09, 2015 Major Error during construction of splicing graph
Bug BARNA-364 Open Unresolved Oct 09, 2015 Minor Flux Capacitor Tool is not found on windows
Bug BARNA-363 Open Unresolved Oct 09, 2015 Major qunatify gene expression of strand-specific data
Bug BARNA-341 Resolved Fixed Oct 09, 2015 Major stabilize profiling in the presence of highly abundant transcripts added to the transcriptome annotation
Improvement BARNA-340 Resolved Fixed Oct 09, 2015 Major implement parameters for annotation sources to be included or excluded in profiling
Bug BARNA-339 Resolved Fixed Oct 09, 2015 Major Array overflow in profiling
Bug BARNA-338 Resolved Fixed Oct 09, 2015 Minor Collapse transcripts that are exactly identical in terms of genomic coordinates of their exons
Improvement BARNA-337 Resolved Fixed Oct 09, 2015 Major Improve profiles stability
Bug BARNA-336 Resolved Fixed Oct 09, 2015 Major SAMException - Value for tag XT is not a Character
Bug BARNA-335 Open Unresolved Oct 09, 2015 Major flux crashes on GTF with spike-ins
Improvement BARNA-334 Resolved Fixed Oct 09, 2015 Major Replace Attributes with Mapping properties
Showing 20 out of 94 issues Refresh

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1 Comment

  1. flux capacitor only returns read counts (or RPKM) even for paired-end reads. Is it planned to ever provide FPKM?

    Best regards,

    Sven