Upcoming JBrowse 1.11.5

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Upcoming JBrowse 1.11.5

Diesh, Colin M.
Hi All,
Here is a list of relevant issues for the JBrowse 1.11.5 release. Please review the list of changes.

ISSUES ADDRESSED IN THIS RELEASE CYCLE

[Fixed] VCF hitting chunkSizeLimit https://github.com/GMOD/jbrowse/issues/486
Summary: Due to an incorrect numerical comparison, jbrowse tries to grab too much content from a VCF file causing chunkSizeLimit errors
Fix: Apply correct numerical comparison
Potential issues: N/A

[Fixed] Forced ASCII sort on (hierarchical) track list https://github.com/GMOD/jbrowse/issues/477
Summary: People might want to prioritize the order of the tracks in the track selector, but the hierarchical track selector sorts by ascii by default.
Fix: add function to optionally disable sort using sortHierarchical=false in the trackSelector section of the config
Potential issues: N/A

[Fixed]Alignments2: detail popup doesn't include TLEN https://github.com/GMOD/jbrowse/issues/471
Summary: the BAM template length (sometimes called insert size?) field was not included in popups
Fix: add template_length field
Potential issues: N/A

[Fixed]Track display mode reverting between chromosomes https://github.com/GMOD/jbrowse/issues/469
Summary: the “compact” displayMode setting isn’t saved when changing chromosomes.
Fix: we implemented a cookie that allows the “display mode” setting to be saved across CanvasFeatures type tracks. 
Potential issues: The cookie only includes the displayMode setting when it could also include other settings too.


[Fixed]Genotypes wrongly displayed in VCF tracks 
Summary: the genotype in the VCF popups was only displaying one allele in the genotype panel
Fix: since this used to work in the 1.10.x branch, by referencing the old codebase, we updated the 1.11.x codebase to fix it
Potential issues: N/A

[Fixed]linkTemplate and/or onClick support for XYPlot track types
Summary:allows configurable onClick and on* methods for Wiggle type tracks
Fix: Incorporation of code from similar track types into the WiggleBase by Richard
Potential issues: N/A

[Feature]Additional customizations to dialog boxes https://github.com/GMOD/jbrowse/issues/494
Summary: many other customizations are possible in the view details popup boxes
See issue page for details

OTHER CHANGES MADE DURING THIS RELEASE CYCLE:

- [Reverted dialog scrolling fix] A earlier fix to make the dialogs scrolling better has been REVERTED due to other consequences that it caused.  
Result is that the original bug is now going to be present, but this is probably for the best for now.

- [Small] data from trackMetadata.csv is now used in hierarchical track selector for categories. See https://github.com/GMOD/jbrowse/commit/78157b5e3c38f0d774fd4ead3213fc8ebbbf0ad6

- [Documentation] the initialSortColumn was not documented in the JBrowse config guide for the faceted track selector. An example of it’s use was added to the jbrowse.conf  and it was also added to http://gmod.org/wiki/JBrowse_Configuration_Guide#Faceted_Track_Selector

- [Feature enhancement] 

- [Small] some CSS was fixed by rdhayes

- [Small] some Makefile compatibility between linux and OSX was addressed by cmdcolin and rdhayes


PROPOSED UNMERGED CHANGES
Both  https://github.com/GMOD/jbrowse/pull/485 and https://github.com/GMOD/jbrowse/pull/473 offer helpful solutions for fixing RNA-seq strand parsing with certain types of aligners. I think combining both pull requests would be ideal to support both XS and  multi segment reads.

Provides an implementation fasta indexed files to be used instead of normal conversion to json. 

SHORT LIST OF OTHER ISSUES FOUND DURING THIS RELEASE CYCLE THAT ARE BEING POSTPONED
GenBank files have problems with certain refseqs in BioPerl 1.6.923.
Users have requested that the track label be repositioned in the genome view.
Inconsistency with floating point view boundaries in the “API" should be addressed.


-Colin
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Re: Upcoming JBrowse 1.11.5

Diesh, Colin M.
Hello,
Several additional changes have occurred for this release cycle.

1) the —refs flag was broken in prepare-refseqs.pl so a fix was contributed by a user. now included
2) there is a proposed fix for the generate-names.pl —incremental fix. this is included but is pending testing.
3) examples for event handlers on wiggle tracks, customized dialog boxes, and multiline callbacks in tracks.conf format files were added

A new testing version is deployed on dropbox temporarily:

c744889353422642539010fb5cc03f02271afa07  https://www.dropbox.com/s/bjuwnpdboobb3cy/JBrowse-1.11.5-dev.zip
804acd92970aa183db61786978bbb1bd0113bb4d  https://www.dropbox.com/s/4dhx53mgsn0stdg/JBrowse-1.11.5.zip

-Colin


Note: we have also had continued discussions about the use of the XS flag for strand parsing and automatic reversal for paired end sequencing. This has not been included in this build.



On Jul 21, 2014, at 9:02 AM, Colin D <[hidden email]> wrote:

Hi All,
Here is a list of relevant issues for the JBrowse 1.11.5 release. Please review the list of changes.

ISSUES ADDRESSED IN THIS RELEASE CYCLE

[Fixed] VCF hitting chunkSizeLimit https://github.com/GMOD/jbrowse/issues/486
Summary: Due to an incorrect numerical comparison, jbrowse tries to grab too much content from a VCF file causing chunkSizeLimit errors
Fix: Apply correct numerical comparison
Potential issues: N/A

[Fixed] Forced ASCII sort on (hierarchical) track list https://github.com/GMOD/jbrowse/issues/477
Summary: People might want to prioritize the order of the tracks in the track selector, but the hierarchical track selector sorts by ascii by default.
Fix: add function to optionally disable sort using sortHierarchical=false in the trackSelector section of the config
Potential issues: N/A

[Fixed]Alignments2: detail popup doesn't include TLEN https://github.com/GMOD/jbrowse/issues/471
Summary: the BAM template length (sometimes called insert size?) field was not included in popups
Fix: add template_length field
Potential issues: N/A

[Fixed]Track display mode reverting between chromosomes https://github.com/GMOD/jbrowse/issues/469
Summary: the “compact” displayMode setting isn’t saved when changing chromosomes.
Fix: we implemented a cookie that allows the “display mode” setting to be saved across CanvasFeatures type tracks. 
Potential issues: The cookie only includes the displayMode setting when it could also include other settings too.


[Fixed]Genotypes wrongly displayed in VCF tracks 
Summary: the genotype in the VCF popups was only displaying one allele in the genotype panel
Fix: since this used to work in the 1.10.x branch, by referencing the old codebase, we updated the 1.11.x codebase to fix it
Potential issues: N/A

[Fixed]linkTemplate and/or onClick support for XYPlot track types
Summary:allows configurable onClick and on* methods for Wiggle type tracks
Fix: Incorporation of code from similar track types into the WiggleBase by Richard
Potential issues: N/A

[Feature]Additional customizations to dialog boxes https://github.com/GMOD/jbrowse/issues/494
Summary: many other customizations are possible in the view details popup boxes
See issue page for details

OTHER CHANGES MADE DURING THIS RELEASE CYCLE:

- [Reverted dialog scrolling fix] A earlier fix to make the dialogs scrolling better has been REVERTED due to other consequences that it caused.  
Result is that the original bug is now going to be present, but this is probably for the best for now.

- [Small] data from trackMetadata.csv is now used in hierarchical track selector for categories. See https://github.com/GMOD/jbrowse/commit/78157b5e3c38f0d774fd4ead3213fc8ebbbf0ad6

- [Documentation] the initialSortColumn was not documented in the JBrowse config guide for the faceted track selector. An example of it’s use was added to the jbrowse.conf  and it was also added to http://gmod.org/wiki/JBrowse_Configuration_Guide#Faceted_Track_Selector

- [Feature enhancement] 

- [Small] some CSS was fixed by rdhayes

- [Small] some Makefile compatibility between linux and OSX was addressed by cmdcolin and rdhayes


PROPOSED UNMERGED CHANGES
Both  https://github.com/GMOD/jbrowse/pull/485 and https://github.com/GMOD/jbrowse/pull/473 offer helpful solutions for fixing RNA-seq strand parsing with certain types of aligners. I think combining both pull requests would be ideal to support both XS and  multi segment reads.

Provides an implementation fasta indexed files to be used instead of normal conversion to json. 

SHORT LIST OF OTHER ISSUES FOUND DURING THIS RELEASE CYCLE THAT ARE BEING POSTPONED
GenBank files have problems with certain refseqs in BioPerl 1.6.923.
Users have requested that the track label be repositioned in the genome view.
Inconsistency with floating point view boundaries in the “API" should be addressed.


-Colin