Upcoming JBrowse 1.11.6

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Upcoming JBrowse 1.11.6

Diesh, Colin M.
Hello all,
I would like to request feedback on the upcoming JBrowse release


The full release notes are here:


I have a list of highlighted changes that might be of interest.


BAM - Fixed SNPs calculations from MD string on hard-clipped and spliced reads (issue #516) (issue #523).
BAM - Allow for reversing the template reads in RNA-seq (!) This is a highly requested feature, including from the Web Apollo group, and allows for much better strand visualization of RNA-seq (issue #485).
BAM - Removal of XS from BAM strand calculation: previously the strand for BAM files included the XS tag, which is a top hat specific tag for indicating the strand of certain reads, and the consensus was that this should be removed (issue #520).
BigWig - new “max” or “min” summary views. Due to problems with “spiky” data, this option was added, and it can help with viewing peaks when these datasets are zoomed out. (i.e. TSS data,  GWAS bigwigs, etc). 
BigWig - Added "log scale” checkbox to bigwig tracks. 
VCF - Fixed "No call” variants: Variant callers can report “no-call” or ‘./.’ and this type of variant would look strange in the pop-up boxes (issue #513).
VCF - Fixed Alternative alleles report: previously we would report that a variant was A,T / A,T instead of choosing which allele was called, so now for example it will select the correct alternative allele and report T/A if the info field contains 1/0 (issue #533).
VCF - Allow for Haploid genomes: previously, if a VCF from a haploid organism was opened, it crashed.
Command line - Incremental indexing fixed: generate-names had a problem and searching for a feature brought up the wrong track, so that was fixed (issue #526).
Command line - Allow for building jbrowse without running perl tests. This is a feature that was requested by the Web Apollo group to facilitate Maven builds .
Command line - Allow for loading files from file paths with weird characters.
UI - Better placement of extra content in the menu bar (awaiting).
UI - Added mouseover customization: some basic mouseover customization is available for HTMLFeatures and CanvasFeatures tracks (issue #480).
UI - Fix a implementation for “shortDescription” to be used in mouseovers on the Hierarchical track list (issue #553).


The only outstanding issue on the dashboard was this one https://github.com/GMOD/jbrowse/issues/540 which occurs when we are trying to calculate “stats” for a track and the stats calculation encounters a chunkSizeError, but since chunkSizeLimit is configurable, this may be moved out.



Thanks
-Colin


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Re: Upcoming JBrowse 1.11.6

Ian Holmes-2
Thanks Colin! This looks good.
I have a question about the customization of content in the menu bar; is this intended to (for example) allow admins to customize the Help menu?
Best, Ian

On Fri, Feb 6, 2015 at 4:53 PM, Diesh, Colin M. <[hidden email]> wrote:
Hello all,
I would like to request feedback on the upcoming JBrowse release


The full release notes are here:


I have a list of highlighted changes that might be of interest.


BAM - Fixed SNPs calculations from MD string on hard-clipped and spliced reads (issue #516) (issue #523).
BAM - Allow for reversing the template reads in RNA-seq (!) This is a highly requested feature, including from the Web Apollo group, and allows for much better strand visualization of RNA-seq (issue #485).
BAM - Removal of XS from BAM strand calculation: previously the strand for BAM files included the XS tag, which is a top hat specific tag for indicating the strand of certain reads, and the consensus was that this should be removed (issue #520).
BigWig - new “max” or “min” summary views. Due to problems with “spiky” data, this option was added, and it can help with viewing peaks when these datasets are zoomed out. (i.e. TSS data,  GWAS bigwigs, etc). 
BigWig - Added "log scale” checkbox to bigwig tracks. 
VCF - Fixed "No call” variants: Variant callers can report “no-call” or ‘./.’ and this type of variant would look strange in the pop-up boxes (issue #513).
VCF - Fixed Alternative alleles report: previously we would report that a variant was A,T / A,T instead of choosing which allele was called, so now for example it will select the correct alternative allele and report T/A if the info field contains 1/0 (issue #533).
VCF - Allow for Haploid genomes: previously, if a VCF from a haploid organism was opened, it crashed.
Command line - Incremental indexing fixed: generate-names had a problem and searching for a feature brought up the wrong track, so that was fixed (issue #526).
Command line - Allow for building jbrowse without running perl tests. This is a feature that was requested by the Web Apollo group to facilitate Maven builds .
Command line - Allow for loading files from file paths with weird characters.
UI - Better placement of extra content in the menu bar (awaiting).
UI - Added mouseover customization: some basic mouseover customization is available for HTMLFeatures and CanvasFeatures tracks (issue #480).
UI - Fix a implementation for “shortDescription” to be used in mouseovers on the Hierarchical track list (issue #553).


The only outstanding issue on the dashboard was this one https://github.com/GMOD/jbrowse/issues/540 which occurs when we are trying to calculate “stats” for a track and the stats calculation encounters a chunkSizeError, but since chunkSizeLimit is configurable, this may be moved out.



Thanks
-Colin



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Re: Upcoming JBrowse 1.11.6

Diesh, Colin M.
The menu bar change that was mentioned is relevant to some work that Richard did (he may be able to explain better). There are actually some existing options since JBrowse 1.9 for customizing the help popup ( “browser.config.quickHelp” ) and WA started using this recently.

However, there is another issue which is a new configuration option called “browser.config.show_menu” in JBrowse 1.11.6. This was requested to allow WA 2.0 to use JBrowse in embedded mode and then to create a custom menu bar outside the iframe.

Here is the original feature request


I can imagine that the “show_menu” option could be controversial so if there any objections let me know.


Thanks,
-Colin


On Feb 10, 2015, at 5:59 PM, Ian Holmes <[hidden email]> wrote:

Thanks Colin! This looks good.
I have a question about the customization of content in the menu bar; is this intended to (for example) allow admins to customize the Help menu?
Best, Ian

On Fri, Feb 6, 2015 at 4:53 PM, Diesh, Colin M. <[hidden email]> wrote:
Hello all,
I would like to request feedback on the upcoming JBrowse release


The full release notes are here:


I have a list of highlighted changes that might be of interest.


BAM - Fixed SNPs calculations from MD string on hard-clipped and spliced reads (issue #516) (issue #523).
BAM - Allow for reversing the template reads in RNA-seq (!) This is a highly requested feature, including from the Web Apollo group, and allows for much better strand visualization of RNA-seq (issue #485).
BAM - Removal of XS from BAM strand calculation: previously the strand for BAM files included the XS tag, which is a top hat specific tag for indicating the strand of certain reads, and the consensus was that this should be removed (issue #520).
BigWig - new “max” or “min” summary views. Due to problems with “spiky” data, this option was added, and it can help with viewing peaks when these datasets are zoomed out. (i.e. TSS data,  GWAS bigwigs, etc). 
BigWig - Added "log scale” checkbox to bigwig tracks. 
VCF - Fixed "No call” variants: Variant callers can report “no-call” or ‘./.’ and this type of variant would look strange in the pop-up boxes (issue #513).
VCF - Fixed Alternative alleles report: previously we would report that a variant was A,T / A,T instead of choosing which allele was called, so now for example it will select the correct alternative allele and report T/A if the info field contains 1/0 (issue #533).
VCF - Allow for Haploid genomes: previously, if a VCF from a haploid organism was opened, it crashed.
Command line - Incremental indexing fixed: generate-names had a problem and searching for a feature brought up the wrong track, so that was fixed (issue #526).
Command line - Allow for building jbrowse without running perl tests. This is a feature that was requested by the Web Apollo group to facilitate Maven builds .
Command line - Allow for loading files from file paths with weird characters.
UI - Better placement of extra content in the menu bar (awaiting).
UI - Added mouseover customization: some basic mouseover customization is available for HTMLFeatures and CanvasFeatures tracks (issue #480).
UI - Fix a implementation for “shortDescription” to be used in mouseovers on the Hierarchical track list (issue #553).


The only outstanding issue on the dashboard was this one https://github.com/GMOD/jbrowse/issues/540 which occurs when we are trying to calculate “stats” for a track and the stats calculation encounters a chunkSizeError, but since chunkSizeLimit is configurable, this may be moved out.



Thanks
-Colin




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Re: Upcoming JBrowse 1.11.6

Diesh, Colin M.
I guess my concern is that people would hide the menu bar for no reason.

We could remove the show_menu from the configuration for now, and then simply make it so that WA can activate via the plugin if needed.

-Colin


On Feb 10, 2015, at 8:53 PM, Diesh, Colin M. <[hidden email]> wrote:

The menu bar change that was mentioned is relevant to some work that Richard did (he may be able to explain better). There are actually some existing options since JBrowse 1.9 for customizing the help popup ( “browser.config.quickHelp” ) and WA started using this recently.

However, there is another issue which is a new configuration option called “browser.config.show_menu” in JBrowse 1.11.6. This was requested to allow WA 2.0 to use JBrowse in embedded mode and then to create a custom menu bar outside the iframe.

Here is the original feature request


I can imagine that the “show_menu” option could be controversial so if there any objections let me know.


Thanks,
-Colin


On Feb 10, 2015, at 5:59 PM, Ian Holmes <[hidden email]> wrote:

Thanks Colin! This looks good.
I have a question about the customization of content in the menu bar; is this intended to (for example) allow admins to customize the Help menu?
Best, Ian

On Fri, Feb 6, 2015 at 4:53 PM, Diesh, Colin M. <[hidden email]> wrote:
Hello all,
I would like to request feedback on the upcoming JBrowse release


The full release notes are here:


I have a list of highlighted changes that might be of interest.


BAM - Fixed SNPs calculations from MD string on hard-clipped and spliced reads (issue #516) (issue #523).
BAM - Allow for reversing the template reads in RNA-seq (!) This is a highly requested feature, including from the Web Apollo group, and allows for much better strand visualization of RNA-seq (issue #485).
BAM - Removal of XS from BAM strand calculation: previously the strand for BAM files included the XS tag, which is a top hat specific tag for indicating the strand of certain reads, and the consensus was that this should be removed (issue #520).
BigWig - new “max” or “min” summary views. Due to problems with “spiky” data, this option was added, and it can help with viewing peaks when these datasets are zoomed out. (i.e. TSS data,  GWAS bigwigs, etc). 
BigWig - Added "log scale” checkbox to bigwig tracks. 
VCF - Fixed "No call” variants: Variant callers can report “no-call” or ‘./.’ and this type of variant would look strange in the pop-up boxes (issue #513).
VCF - Fixed Alternative alleles report: previously we would report that a variant was A,T / A,T instead of choosing which allele was called, so now for example it will select the correct alternative allele and report T/A if the info field contains 1/0 (issue #533).
VCF - Allow for Haploid genomes: previously, if a VCF from a haploid organism was opened, it crashed.
Command line - Incremental indexing fixed: generate-names had a problem and searching for a feature brought up the wrong track, so that was fixed (issue #526).
Command line - Allow for building jbrowse without running perl tests. This is a feature that was requested by the Web Apollo group to facilitate Maven builds .
Command line - Allow for loading files from file paths with weird characters.
UI - Better placement of extra content in the menu bar (awaiting).
UI - Added mouseover customization: some basic mouseover customization is available for HTMLFeatures and CanvasFeatures tracks (issue #480).
UI - Fix a implementation for “shortDescription” to be used in mouseovers on the Hierarchical track list (issue #553).


The only outstanding issue on the dashboard was this one https://github.com/GMOD/jbrowse/issues/540 which occurs when we are trying to calculate “stats” for a track and the stats calculation encounters a chunkSizeError, but since chunkSizeLimit is configurable, this may be moved out.



Thanks
-Colin





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Re: Upcoming JBrowse 1.11.6

Diesh, Colin M.
In reply to this post by Diesh, Colin M.
I guess my concern is that people would hide the menu bar for no reason.

We could remove the show_menu from the configuration for now, and then simply make it so that WA can activate via the plugin if needed.

-Colin


On Feb 10, 2015, at 8:53 PM, Diesh, Colin M. <[hidden email]> wrote:

The menu bar change that was mentioned is relevant to some work that Richard did (he may be able to explain better). There are actually some existing options since JBrowse 1.9 for customizing the help popup ( “browser.config.quickHelp” ) and WA started using this recently.

However, there is another issue which is a new configuration option called “browser.config.show_menu” in JBrowse 1.11.6. This was requested to allow WA 2.0 to use JBrowse in embedded mode and then to create a custom menu bar outside the iframe.

Here is the original feature request


I can imagine that the “show_menu” option could be controversial so if there any objections let me know.


Thanks,
-Colin


On Feb 10, 2015, at 5:59 PM, Ian Holmes <[hidden email]> wrote:

Thanks Colin! This looks good.
I have a question about the customization of content in the menu bar; is this intended to (for example) allow admins to customize the Help menu?
Best, Ian

On Fri, Feb 6, 2015 at 4:53 PM, Diesh, Colin M. <[hidden email]> wrote:
Hello all,
I would like to request feedback on the upcoming JBrowse release


The full release notes are here:


I have a list of highlighted changes that might be of interest.


BAM - Fixed SNPs calculations from MD string on hard-clipped and spliced reads (issue #516) (issue #523).
BAM - Allow for reversing the template reads in RNA-seq (!) This is a highly requested feature, including from the Web Apollo group, and allows for much better strand visualization of RNA-seq (issue #485).
BAM - Removal of XS from BAM strand calculation: previously the strand for BAM files included the XS tag, which is a top hat specific tag for indicating the strand of certain reads, and the consensus was that this should be removed (issue #520).
BigWig - new “max” or “min” summary views. Due to problems with “spiky” data, this option was added, and it can help with viewing peaks when these datasets are zoomed out. (i.e. TSS data,  GWAS bigwigs, etc). 
BigWig - Added "log scale” checkbox to bigwig tracks. 
VCF - Fixed "No call” variants: Variant callers can report “no-call” or ‘./.’ and this type of variant would look strange in the pop-up boxes (issue #513).
VCF - Fixed Alternative alleles report: previously we would report that a variant was A,T / A,T instead of choosing which allele was called, so now for example it will select the correct alternative allele and report T/A if the info field contains 1/0 (issue #533).
VCF - Allow for Haploid genomes: previously, if a VCF from a haploid organism was opened, it crashed.
Command line - Incremental indexing fixed: generate-names had a problem and searching for a feature brought up the wrong track, so that was fixed (issue #526).
Command line - Allow for building jbrowse without running perl tests. This is a feature that was requested by the Web Apollo group to facilitate Maven builds .
Command line - Allow for loading files from file paths with weird characters.
UI - Better placement of extra content in the menu bar (awaiting).
UI - Added mouseover customization: some basic mouseover customization is available for HTMLFeatures and CanvasFeatures tracks (issue #480).
UI - Fix a implementation for “shortDescription” to be used in mouseovers on the Hierarchical track list (issue #553).


The only outstanding issue on the dashboard was this one https://github.com/GMOD/jbrowse/issues/540 which occurs when we are trying to calculate “stats” for a track and the stats calculation encounters a chunkSizeError, but since chunkSizeLimit is configurable, this may be moved out.



Thanks
-Colin





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Re: Upcoming JBrowse 1.11.6

nathandunn
In reply to this post by Diesh, Colin M.

The “show_menu” is for WA 1 (and 2).   So long as its an option and not the default I think its a good feature that helps users embed it. 

Nathan

On Feb 10, 2015, at 10:37 PM, Diesh, Colin M. <[hidden email]> wrote:

I guess my concern is that people would hide the menu bar for no reason.

We could remove the show_menu from the configuration for now, and then simply make it so that WA can activate via the plugin if needed.

-Colin


On Feb 10, 2015, at 8:53 PM, Diesh, Colin M. <[hidden email]> wrote:

The menu bar change that was mentioned is relevant to some work that Richard did (he may be able to explain better). There are actually some existing options since JBrowse 1.9 for customizing the help popup ( “browser.config.quickHelp” ) and WA started using this recently.

However, there is another issue which is a new configuration option called “browser.config.show_menu” in JBrowse 1.11.6. This was requested to allow WA 2.0 to use JBrowse in embedded mode and then to create a custom menu bar outside the iframe.

Here is the original feature request


I can imagine that the “show_menu” option could be controversial so if there any objections let me know.


Thanks,
-Colin


On Feb 10, 2015, at 5:59 PM, Ian Holmes <[hidden email]> wrote:

Thanks Colin! This looks good.
I have a question about the customization of content in the menu bar; is this intended to (for example) allow admins to customize the Help menu?
Best, Ian

On Fri, Feb 6, 2015 at 4:53 PM, Diesh, Colin M. <[hidden email]> wrote:
Hello all,
I would like to request feedback on the upcoming JBrowse release


The full release notes are here:


I have a list of highlighted changes that might be of interest.


BAM - Fixed SNPs calculations from MD string on hard-clipped and spliced reads (issue #516) (issue #523).
BAM - Allow for reversing the template reads in RNA-seq (!) This is a highly requested feature, including from the Web Apollo group, and allows for much better strand visualization of RNA-seq (issue #485).
BAM - Removal of XS from BAM strand calculation: previously the strand for BAM files included the XS tag, which is a top hat specific tag for indicating the strand of certain reads, and the consensus was that this should be removed (issue #520).
BigWig - new “max” or “min” summary views. Due to problems with “spiky” data, this option was added, and it can help with viewing peaks when these datasets are zoomed out. (i.e. TSS data,  GWAS bigwigs, etc). 
BigWig - Added "log scale” checkbox to bigwig tracks. 
VCF - Fixed "No call” variants: Variant callers can report “no-call” or ‘./.’ and this type of variant would look strange in the pop-up boxes (issue #513).
VCF - Fixed Alternative alleles report: previously we would report that a variant was A,T / A,T instead of choosing which allele was called, so now for example it will select the correct alternative allele and report T/A if the info field contains 1/0 (issue #533).
VCF - Allow for Haploid genomes: previously, if a VCF from a haploid organism was opened, it crashed.
Command line - Incremental indexing fixed: generate-names had a problem and searching for a feature brought up the wrong track, so that was fixed (issue #526).
Command line - Allow for building jbrowse without running perl tests. This is a feature that was requested by the Web Apollo group to facilitate Maven builds .
Command line - Allow for loading files from file paths with weird characters.
UI - Better placement of extra content in the menu bar (awaiting).
UI - Added mouseover customization: some basic mouseover customization is available for HTMLFeatures and CanvasFeatures tracks (issue #480).
UI - Fix a implementation for “shortDescription” to be used in mouseovers on the Hierarchical track list (issue #553).


The only outstanding issue on the dashboard was this one https://github.com/GMOD/jbrowse/issues/540 which occurs when we are trying to calculate “stats” for a track and the stats calculation encounters a chunkSizeError, but since chunkSizeLimit is configurable, this may be moved out.



Thanks
-Colin






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Re: Upcoming JBrowse 1.11.6

Diesh, Colin M.
I would agree with Nathan but I just wanted to mention it to make sure.


I have sent beta versions out to Deepak, Richard and Nathan for testing in the meantime and expect that a release could be done by the end of the week.



-Colin


On Feb 11, 2015, at 7:40 AM, Nathan Dunn <[hidden email]> wrote:


The “show_menu” is for WA 1 (and 2).   So long as its an option and not the default I think its a good feature that helps users embed it. 

Nathan

On Feb 10, 2015, at 10:37 PM, Diesh, Colin M. <[hidden email]> wrote:

I guess my concern is that people would hide the menu bar for no reason.

We could remove the show_menu from the configuration for now, and then simply make it so that WA can activate via the plugin if needed.

-Colin


On Feb 10, 2015, at 8:53 PM, Diesh, Colin M. <[hidden email]> wrote:

The menu bar change that was mentioned is relevant to some work that Richard did (he may be able to explain better). There are actually some existing options since JBrowse 1.9 for customizing the help popup ( “browser.config.quickHelp” ) and WA started using this recently.

However, there is another issue which is a new configuration option called “browser.config.show_menu” in JBrowse 1.11.6. This was requested to allow WA 2.0 to use JBrowse in embedded mode and then to create a custom menu bar outside the iframe.

Here is the original feature request


I can imagine that the “show_menu” option could be controversial so if there any objections let me know.


Thanks,
-Colin


On Feb 10, 2015, at 5:59 PM, Ian Holmes <[hidden email]> wrote:

Thanks Colin! This looks good.
I have a question about the customization of content in the menu bar; is this intended to (for example) allow admins to customize the Help menu?
Best, Ian

On Fri, Feb 6, 2015 at 4:53 PM, Diesh, Colin M. <[hidden email]> wrote:
Hello all,
I would like to request feedback on the upcoming JBrowse release


The full release notes are here:


I have a list of highlighted changes that might be of interest.


BAM - Fixed SNPs calculations from MD string on hard-clipped and spliced reads (issue #516) (issue #523).
BAM - Allow for reversing the template reads in RNA-seq (!) This is a highly requested feature, including from the Web Apollo group, and allows for much better strand visualization of RNA-seq (issue #485).
BAM - Removal of XS from BAM strand calculation: previously the strand for BAM files included the XS tag, which is a top hat specific tag for indicating the strand of certain reads, and the consensus was that this should be removed (issue #520).
BigWig - new “max” or “min” summary views. Due to problems with “spiky” data, this option was added, and it can help with viewing peaks when these datasets are zoomed out. (i.e. TSS data,  GWAS bigwigs, etc). 
BigWig - Added "log scale” checkbox to bigwig tracks. 
VCF - Fixed "No call” variants: Variant callers can report “no-call” or ‘./.’ and this type of variant would look strange in the pop-up boxes (issue #513).
VCF - Fixed Alternative alleles report: previously we would report that a variant was A,T / A,T instead of choosing which allele was called, so now for example it will select the correct alternative allele and report T/A if the info field contains 1/0 (issue #533).
VCF - Allow for Haploid genomes: previously, if a VCF from a haploid organism was opened, it crashed.
Command line - Incremental indexing fixed: generate-names had a problem and searching for a feature brought up the wrong track, so that was fixed (issue #526).
Command line - Allow for building jbrowse without running perl tests. This is a feature that was requested by the Web Apollo group to facilitate Maven builds .
Command line - Allow for loading files from file paths with weird characters.
UI - Better placement of extra content in the menu bar (awaiting).
UI - Added mouseover customization: some basic mouseover customization is available for HTMLFeatures and CanvasFeatures tracks (issue #480).
UI - Fix a implementation for “shortDescription” to be used in mouseovers on the Hierarchical track list (issue #553).


The only outstanding issue on the dashboard was this one https://github.com/GMOD/jbrowse/issues/540 which occurs when we are trying to calculate “stats” for a track and the stats calculation encounters a chunkSizeError, but since chunkSizeLimit is configurable, this may be moved out.



Thanks
-Colin







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Re: Upcoming JBrowse 1.11.6

Richard Hayes
In reply to this post by Diesh, Colin M.

On Tue, Feb 10, 2015 at 6:53 PM, Diesh, Colin M. <[hidden email]> wrote:
The menu bar change that was mentioned is relevant to some work that Richard did (he may be able to explain better). There are actually some existing options since JBrowse 1.9 for customizing the help popup ( “browser.config.quickHelp” ) and WA started using this recently.

My commit to menubar.css only reorients the existing menu components to allow better display of any additional DIVs added on via plugin code. Our example usage is the addition of the Phytozome logo to the right side so we have a link back to our homepage:
http://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes%2FEgrandis
 

However, there is another issue which is a new configuration option called “browser.config.show_menu” in JBrowse 1.11.6. This was requested to allow WA 2.0 to use JBrowse in embedded mode and then to create a custom menu bar outside the iframe.

Here is the original feature request


I can imagine that the “show_menu” option could be controversial so if there any objections let me know.

Does show_menu effectively work by setting nav, tracklist, and overview to 0 with a single parameter? I haven't been following the discussion of this issue very closely.



Thanks,
-Colin


On Feb 10, 2015, at 5:59 PM, Ian Holmes <[hidden email]> wrote:

Thanks Colin! This looks good.
I have a question about the customization of content in the menu bar; is this intended to (for example) allow admins to customize the Help menu?
Best, Ian

On Fri, Feb 6, 2015 at 4:53 PM, Diesh, Colin M. <[hidden email]> wrote:
Hello all,
I would like to request feedback on the upcoming JBrowse release


The full release notes are here:


I have a list of highlighted changes that might be of interest.


BAM - Fixed SNPs calculations from MD string on hard-clipped and spliced reads (issue #516) (issue #523).
BAM - Allow for reversing the template reads in RNA-seq (!) This is a highly requested feature, including from the Web Apollo group, and allows for much better strand visualization of RNA-seq (issue #485).
BAM - Removal of XS from BAM strand calculation: previously the strand for BAM files included the XS tag, which is a top hat specific tag for indicating the strand of certain reads, and the consensus was that this should be removed (issue #520).
BigWig - new “max” or “min” summary views. Due to problems with “spiky” data, this option was added, and it can help with viewing peaks when these datasets are zoomed out. (i.e. TSS data,  GWAS bigwigs, etc). 
BigWig - Added "log scale” checkbox to bigwig tracks. 
VCF - Fixed "No call” variants: Variant callers can report “no-call” or ‘./.’ and this type of variant would look strange in the pop-up boxes (issue #513).
VCF - Fixed Alternative alleles report: previously we would report that a variant was A,T / A,T instead of choosing which allele was called, so now for example it will select the correct alternative allele and report T/A if the info field contains 1/0 (issue #533).
VCF - Allow for Haploid genomes: previously, if a VCF from a haploid organism was opened, it crashed.
Command line - Incremental indexing fixed: generate-names had a problem and searching for a feature brought up the wrong track, so that was fixed (issue #526).
Command line - Allow for building jbrowse without running perl tests. This is a feature that was requested by the Web Apollo group to facilitate Maven builds .
Command line - Allow for loading files from file paths with weird characters.
UI - Better placement of extra content in the menu bar (awaiting).
UI - Added mouseover customization: some basic mouseover customization is available for HTMLFeatures and CanvasFeatures tracks (issue #480).
UI - Fix a implementation for “shortDescription” to be used in mouseovers on the Hierarchical track list (issue #553).


The only outstanding issue on the dashboard was this one https://github.com/GMOD/jbrowse/issues/540 which occurs when we are trying to calculate “stats” for a track and the stats calculation encounters a chunkSizeError, but since chunkSizeLimit is configurable, this may be moved out.



Thanks
-Colin





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Re: Upcoming JBrowse 1.11.6

Diesh, Colin M.
The show_menu option only removes the main menu bar whereas the show_nav option hides the main menu bar and the navigation options (zoom button, etc).

The nav=0 option also produces the “view in full screen” button but the show_menu option does not. 

-Colin


On Feb 11, 2015, at 1:24 PM, Richard Hayes <[hidden email]> wrote:


On Tue, Feb 10, 2015 at 6:53 PM, Diesh, Colin M. <[hidden email]> wrote:
The menu bar change that was mentioned is relevant to some work that Richard did (he may be able to explain better). There are actually some existing options since JBrowse 1.9 for customizing the help popup ( “browser.config.quickHelp” ) and WA started using this recently.

My commit to menubar.css only reorients the existing menu components to allow better display of any additional DIVs added on via plugin code. Our example usage is the addition of the Phytozome logo to the right side so we have a link back to our homepage:
http://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes%2FEgrandis
 

However, there is another issue which is a new configuration option called “browser.config.show_menu” in JBrowse 1.11.6. This was requested to allow WA 2.0 to use JBrowse in embedded mode and then to create a custom menu bar outside the iframe.

Here is the original feature request


I can imagine that the “show_menu” option could be controversial so if there any objections let me know.

Does show_menu effectively work by setting nav, tracklist, and overview to 0 with a single parameter? I haven't been following the discussion of this issue very closely.



Thanks,
-Colin


On Feb 10, 2015, at 5:59 PM, Ian Holmes <[hidden email]> wrote:

Thanks Colin! This looks good.
I have a question about the customization of content in the menu bar; is this intended to (for example) allow admins to customize the Help menu?
Best, Ian

On Fri, Feb 6, 2015 at 4:53 PM, Diesh, Colin M. <[hidden email]> wrote:
Hello all,
I would like to request feedback on the upcoming JBrowse release


The full release notes are here:


I have a list of highlighted changes that might be of interest.


BAM - Fixed SNPs calculations from MD string on hard-clipped and spliced reads (issue #516) (issue #523).
BAM - Allow for reversing the template reads in RNA-seq (!) This is a highly requested feature, including from the Web Apollo group, and allows for much better strand visualization of RNA-seq (issue #485).
BAM - Removal of XS from BAM strand calculation: previously the strand for BAM files included the XS tag, which is a top hat specific tag for indicating the strand of certain reads, and the consensus was that this should be removed (issue #520).
BigWig - new “max” or “min” summary views. Due to problems with “spiky” data, this option was added, and it can help with viewing peaks when these datasets are zoomed out. (i.e. TSS data,  GWAS bigwigs, etc). 
BigWig - Added "log scale” checkbox to bigwig tracks. 
VCF - Fixed "No call” variants: Variant callers can report “no-call” or ‘./.’ and this type of variant would look strange in the pop-up boxes (issue #513).
VCF - Fixed Alternative alleles report: previously we would report that a variant was A,T / A,T instead of choosing which allele was called, so now for example it will select the correct alternative allele and report T/A if the info field contains 1/0 (issue #533).
VCF - Allow for Haploid genomes: previously, if a VCF from a haploid organism was opened, it crashed.
Command line - Incremental indexing fixed: generate-names had a problem and searching for a feature brought up the wrong track, so that was fixed (issue #526).
Command line - Allow for building jbrowse without running perl tests. This is a feature that was requested by the Web Apollo group to facilitate Maven builds .
Command line - Allow for loading files from file paths with weird characters.
UI - Better placement of extra content in the menu bar (awaiting).
UI - Added mouseover customization: some basic mouseover customization is available for HTMLFeatures and CanvasFeatures tracks (issue #480).
UI - Fix a implementation for “shortDescription” to be used in mouseovers on the Hierarchical track list (issue #553).


The only outstanding issue on the dashboard was this one https://github.com/GMOD/jbrowse/issues/540 which occurs when we are trying to calculate “stats” for a track and the stats calculation encounters a chunkSizeError, but since chunkSizeLimit is configurable, this may be moved out.



Thanks
-Colin






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Re: Upcoming JBrowse 1.11.6

nathandunn

The nav=0 works fine, except I also want to have it get rid of the login button, as well.  I do like having  it embedded in there, though. 

The show_menu or menu=0 does not work in the URL string (would be great if it did).    Could be I did something wrong, though. 

Nathan

On Feb 11, 2015, at 12:09 PM, Diesh, Colin M. <[hidden email]> wrote:

The show_menu option only removes the main menu bar whereas the show_nav option hides the main menu bar and the navigation options (zoom button, etc).

The nav=0 option also produces the “view in full screen” button but the show_menu option does not. 

-Colin


On Feb 11, 2015, at 1:24 PM, Richard Hayes <[hidden email]> wrote:


On Tue, Feb 10, 2015 at 6:53 PM, Diesh, Colin M. <[hidden email]> wrote:
The menu bar change that was mentioned is relevant to some work that Richard did (he may be able to explain better). There are actually some existing options since JBrowse 1.9 for customizing the help popup ( “browser.config.quickHelp” ) and WA started using this recently.

My commit to menubar.css only reorients the existing menu components to allow better display of any additional DIVs added on via plugin code. Our example usage is the addition of the Phytozome logo to the right side so we have a link back to our homepage:
http://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes%2FEgrandis
 

However, there is another issue which is a new configuration option called “browser.config.show_menu” in JBrowse 1.11.6. This was requested to allow WA 2.0 to use JBrowse in embedded mode and then to create a custom menu bar outside the iframe.

Here is the original feature request


I can imagine that the “show_menu” option could be controversial so if there any objections let me know.

Does show_menu effectively work by setting nav, tracklist, and overview to 0 with a single parameter? I haven't been following the discussion of this issue very closely.



Thanks,
-Colin


On Feb 10, 2015, at 5:59 PM, Ian Holmes <[hidden email]> wrote:

Thanks Colin! This looks good.
I have a question about the customization of content in the menu bar; is this intended to (for example) allow admins to customize the Help menu?
Best, Ian

On Fri, Feb 6, 2015 at 4:53 PM, Diesh, Colin M. <[hidden email]> wrote:
Hello all,
I would like to request feedback on the upcoming JBrowse release


The full release notes are here:


I have a list of highlighted changes that might be of interest.


BAM - Fixed SNPs calculations from MD string on hard-clipped and spliced reads (issue #516) (issue #523).
BAM - Allow for reversing the template reads in RNA-seq (!) This is a highly requested feature, including from the Web Apollo group, and allows for much better strand visualization of RNA-seq (issue #485).
BAM - Removal of XS from BAM strand calculation: previously the strand for BAM files included the XS tag, which is a top hat specific tag for indicating the strand of certain reads, and the consensus was that this should be removed (issue #520).
BigWig - new “max” or “min” summary views. Due to problems with “spiky” data, this option was added, and it can help with viewing peaks when these datasets are zoomed out. (i.e. TSS data,  GWAS bigwigs, etc). 
BigWig - Added "log scale” checkbox to bigwig tracks. 
VCF - Fixed "No call” variants: Variant callers can report “no-call” or ‘./.’ and this type of variant would look strange in the pop-up boxes (issue #513).
VCF - Fixed Alternative alleles report: previously we would report that a variant was A,T / A,T instead of choosing which allele was called, so now for example it will select the correct alternative allele and report T/A if the info field contains 1/0 (issue #533).
VCF - Allow for Haploid genomes: previously, if a VCF from a haploid organism was opened, it crashed.
Command line - Incremental indexing fixed: generate-names had a problem and searching for a feature brought up the wrong track, so that was fixed (issue #526).
Command line - Allow for building jbrowse without running perl tests. This is a feature that was requested by the Web Apollo group to facilitate Maven builds .
Command line - Allow for loading files from file paths with weird characters.
UI - Better placement of extra content in the menu bar (awaiting).
UI - Added mouseover customization: some basic mouseover customization is available for HTMLFeatures and CanvasFeatures tracks (issue #480).
UI - Fix a implementation for “shortDescription” to be used in mouseovers on the Hierarchical track list (issue #553).


The only outstanding issue on the dashboard was this one https://github.com/GMOD/jbrowse/issues/540 which occurs when we are trying to calculate “stats” for a track and the stats calculation encounters a chunkSizeError, but since chunkSizeLimit is configurable, this may be moved out.



Thanks
-Colin