[Gmod-ajax] JBrowse 1.11.3 released

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[Gmod-ajax] JBrowse 1.11.3 released

Robert Buels-2
Hi all,

JBrowse 1.11.3 has been released, with quite a few improvements and
bugfixes, including a new coloring scheme for BAM alignment tracks
(Alignments2 tracks), a fix for some annoying bugs with the feature
arrowheads, and some nice new configuration variables for customizing
the display of certain fields in the default feature detail popup dialog
boxes (see the JBrowse Configuration Guide for details).

It can be downloaded from http://jbrowse.org/jbrowse-1-11-3.

The full release notes:

## Minor improvements

  * Added a "Zoom to this" item in the default right-click menus for
    canvas-based feature tracks.  Thanks to Paul Hale for the initial
    implementation of this.

  * Allow the user to set the document.domain property via jbrowse.conf
    which can be helpful especially if jbrowse is embedded in a iframe.
    Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix
    (issue #440)

  * Improved the graphic design of the "Add sequence search" dialog box
    to make it clearer how to switch between providing an amino acid
    and a nucleotide sequence.  Thanks to Kevin Mohamed for the initial
    implementation of this (issue #436).

  * Expanded the default color set of `Alignments2` tracks to show
    different shades of color indications of reads with missing mate
    pairs, improperly aligned reads, and reads with mate pairs on
    different reference sequences.  Thanks to Keiran Raine for
    implementing this (issue #443).

  * Added support to customize specific parts of the 'View details'
    popups using callback functions. Thanks to Kieran Raine for the
    idea and Colin Diesh for the implementation (issue #421).

  * The File->Open tool will now can add files named `*.coverage.*` or
    `*.density.*` as histograms to newly-opened tracks if the file
    basenames match.  For example, if both `mysample.bam` and
    `mysample.coverage.bw` are present, `mysample.coverage.bw` will be
    added as a histogram source for `mysample.bam`.  Thanks to Keiran
    Raine and Alexander Stoddard for suggesting this (issue #423).

## Bug fixes

  * Fixed a problem where the feature arrowhead would get stuck in the
    middle of the screen at high zoom levels. Thanks to Colin Diesh for
    the fix (issue #449).

  * Disabled the FASTA download button in the "View details" page on
    Safari (issue #412). This feature can't be supported in Safari at
    this time, but it is still supported in most other browsers. Rob
    Buels and Colin Diesh contributed fixes to this issue.

  * Fixed a bug in the client-side GFF3 parser pointed out by Andrew
    Warren.  Thanks Andrew! (issue #452).

  * Fixed the problem of translation frames being switched around at
    different zoom levels. Thanks to Kieron Taylor for the bug report
    and Colin Diesh for the bugfix (issue #435)

  * Fixed a bug where gene features in GFF tracks would not have
    arrowhead markers. Thanks to Colin Diesh for finding and fixing
    this issue (issue #454)


Happy browsing.  ;-)

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org




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Re: JBrowse 1.11.3 released

Robert Buels-2
Hi all,

Forgot to mention:

This will be my last JBrowse release in my position as JBrowse lead
developer.

Thank you all for the past two years of development; we’ve made some
exciting strides, and it’s been great working with you!


Robert Buels
Lead Developer (for a few more hours)
JBrowse - http://jbrowse.org

On 03/07/2014 01:31 PM, Robert Buels wrote:

> Hi all,
>
> JBrowse 1.11.3 has been released, with quite a few improvements and
> bugfixes, including a new coloring scheme for BAM alignment tracks
> (Alignments2 tracks), a fix for some annoying bugs with the feature
> arrowheads, and some nice new configuration variables for customizing
> the display of certain fields in the default feature detail popup dialog
> boxes (see the JBrowse Configuration Guide for details).
>
> It can be downloaded from http://jbrowse.org/jbrowse-1-11-3.
>
> The full release notes:
>
> ## Minor improvements
>
>   * Added a "Zoom to this" item in the default right-click menus for
>     canvas-based feature tracks.  Thanks to Paul Hale for the initial
>     implementation of this.
>
>   * Allow the user to set the document.domain property via jbrowse.conf
>     which can be helpful especially if jbrowse is embedded in a iframe.
>     Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix
>     (issue #440)
>
>   * Improved the graphic design of the "Add sequence search" dialog box
>     to make it clearer how to switch between providing an amino acid
>     and a nucleotide sequence.  Thanks to Kevin Mohamed for the initial
>     implementation of this (issue #436).
>
>   * Expanded the default color set of `Alignments2` tracks to show
>     different shades of color indications of reads with missing mate
>     pairs, improperly aligned reads, and reads with mate pairs on
>     different reference sequences.  Thanks to Keiran Raine for
>     implementing this (issue #443).
>
>   * Added support to customize specific parts of the 'View details'
>     popups using callback functions. Thanks to Kieran Raine for the
>     idea and Colin Diesh for the implementation (issue #421).
>
>   * The File->Open tool will now can add files named `*.coverage.*` or
>     `*.density.*` as histograms to newly-opened tracks if the file
>     basenames match.  For example, if both `mysample.bam` and
>     `mysample.coverage.bw` are present, `mysample.coverage.bw` will be
>     added as a histogram source for `mysample.bam`.  Thanks to Keiran
>     Raine and Alexander Stoddard for suggesting this (issue #423).
>
> ## Bug fixes
>
>   * Fixed a problem where the feature arrowhead would get stuck in the
>     middle of the screen at high zoom levels. Thanks to Colin Diesh for
>     the fix (issue #449).
>
>   * Disabled the FASTA download button in the "View details" page on
>     Safari (issue #412). This feature can't be supported in Safari at
>     this time, but it is still supported in most other browsers. Rob
>     Buels and Colin Diesh contributed fixes to this issue.
>
>   * Fixed a bug in the client-side GFF3 parser pointed out by Andrew
>     Warren.  Thanks Andrew! (issue #452).
>
>   * Fixed the problem of translation frames being switched around at
>     different zoom levels. Thanks to Kieron Taylor for the bug report
>     and Colin Diesh for the bugfix (issue #435)
>
>   * Fixed a bug where gene features in GFF tracks would not have
>     arrowhead markers. Thanks to Colin Diesh for finding and fixing
>     this issue (issue #454)
>
>
> Happy browsing.  ;-)
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
>
>

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freedom to use Git, Perforce or both. Make the move to Perforce.
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Re: JBrowse 1.11.3 released

girlwithglasses
Thank you Rob for making such fantastic progress, and for your tireless devotion to JBrowse and GMOD. On behalf of GMOD, all the very best for the future, and thank you for your hard work!

Amelia
GMOD Community Support


On Fri, Mar 7, 2014 at 10:36 AM, Robert Buels <[hidden email]> wrote:
Hi all,

Forgot to mention:

This will be my last JBrowse release in my position as JBrowse lead
developer.

Thank you all for the past two years of development; we’ve made some
exciting strides, and it’s been great working with you!


Robert Buels
Lead Developer (for a few more hours)
JBrowse - http://jbrowse.org

On 03/07/2014 01:31 PM, Robert Buels wrote:
> Hi all,
>
> JBrowse 1.11.3 has been released, with quite a few improvements and
> bugfixes, including a new coloring scheme for BAM alignment tracks
> (Alignments2 tracks), a fix for some annoying bugs with the feature
> arrowheads, and some nice new configuration variables for customizing
> the display of certain fields in the default feature detail popup dialog
> boxes (see the JBrowse Configuration Guide for details).
>
> It can be downloaded from http://jbrowse.org/jbrowse-1-11-3.
>
> The full release notes:
>
> ## Minor improvements
>
>   * Added a "Zoom to this" item in the default right-click menus for
>     canvas-based feature tracks.  Thanks to Paul Hale for the initial
>     implementation of this.
>
>   * Allow the user to set the document.domain property via jbrowse.conf
>     which can be helpful especially if jbrowse is embedded in a iframe.
>     Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix
>     (issue #440)
>
>   * Improved the graphic design of the "Add sequence search" dialog box
>     to make it clearer how to switch between providing an amino acid
>     and a nucleotide sequence.  Thanks to Kevin Mohamed for the initial
>     implementation of this (issue #436).
>
>   * Expanded the default color set of `Alignments2` tracks to show
>     different shades of color indications of reads with missing mate
>     pairs, improperly aligned reads, and reads with mate pairs on
>     different reference sequences.  Thanks to Keiran Raine for
>     implementing this (issue #443).
>
>   * Added support to customize specific parts of the 'View details'
>     popups using callback functions. Thanks to Kieran Raine for the
>     idea and Colin Diesh for the implementation (issue #421).
>
>   * The File->Open tool will now can add files named `*.coverage.*` or
>     `*.density.*` as histograms to newly-opened tracks if the file
>     basenames match.  For example, if both `mysample.bam` and
>     `mysample.coverage.bw` are present, `mysample.coverage.bw` will be
>     added as a histogram source for `mysample.bam`.  Thanks to Keiran
>     Raine and Alexander Stoddard for suggesting this (issue #423).
>
> ## Bug fixes
>
>   * Fixed a problem where the feature arrowhead would get stuck in the
>     middle of the screen at high zoom levels. Thanks to Colin Diesh for
>     the fix (issue #449).
>
>   * Disabled the FASTA download button in the "View details" page on
>     Safari (issue #412). This feature can't be supported in Safari at
>     this time, but it is still supported in most other browsers. Rob
>     Buels and Colin Diesh contributed fixes to this issue.
>
>   * Fixed a bug in the client-side GFF3 parser pointed out by Andrew
>     Warren.  Thanks Andrew! (issue #452).
>
>   * Fixed the problem of translation frames being switched around at
>     different zoom levels. Thanks to Kieron Taylor for the bug report
>     and Colin Diesh for the bugfix (issue #435)
>
>   * Fixed a bug where gene features in GFF tracks would not have
>     arrowhead markers. Thanks to Colin Diesh for finding and fixing
>     this issue (issue #454)
>
>
> Happy browsing.  ;-)
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
>
>

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--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject


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Re: JBrowse 1.11.3 released

Robert Buels-2
Thanks Amelia!  It's been a real pleasure working with you!  And all the
rest of the GMOD folks!  We've accomplished a lot!

Rob

On 03/07/2014 02:26 PM, Amelia Ireland wrote:
> Thank you Rob for making such fantastic progress, and for your tireless
> devotion to JBrowse and GMOD. On behalf of GMOD, all the very best for
> the future, and thank you for your hard work!
>
> Amelia
> GMOD Community Support

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freedom to use Git, Perforce or both. Make the move to Perforce.
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[Gmod-ajax] Histograms with CanvasFeatures in JBrowse

TROESSER, DANIEL (AG-Contractor/1000)
In reply to this post by Robert Buels-2
Does anyone know how to get pre-generated histogram data to work with CanvasFeatures?  We're using LazyNCList files.  It's generating histograms, but it's generating it from the feature data (lf-{Chunk}.json) rather than hist-xxxxxx-{Chunk}.json.

Thanks,

Dan
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Re: JBrowse 1.11.3 released

Jillian Rowe
In reply to this post by Robert Buels-2
Hi Robert,

It's been great watching Jbrowse grow and change this last year. Myself
and my colleagues truly believe its the best genome browser out there,
opensource or otherwise.

Good luck with all your future endeavors! I'm sure you'll do great!

Best,
Jillian


On 03/07/2014 09:36 PM, Robert Buels wrote:

> Hi all,
>
> Forgot to mention:
>
> This will be my last JBrowse release in my position as JBrowse lead
> developer.
>
> Thank you all for the past two years of development; we’ve made some
> exciting strides, and it’s been great working with you!
>
>
> Robert Buels
> Lead Developer (for a few more hours)
> JBrowse - http://jbrowse.org
>
> On 03/07/2014 01:31 PM, Robert Buels wrote:
>> Hi all,
>>
>> JBrowse 1.11.3 has been released, with quite a few improvements and
>> bugfixes, including a new coloring scheme for BAM alignment tracks
>> (Alignments2 tracks), a fix for some annoying bugs with the feature
>> arrowheads, and some nice new configuration variables for customizing
>> the display of certain fields in the default feature detail popup dialog
>> boxes (see the JBrowse Configuration Guide for details).
>>
>> It can be downloaded from http://jbrowse.org/jbrowse-1-11-3.
>>
>> The full release notes:
>>
>> ## Minor improvements
>>
>>    * Added a "Zoom to this" item in the default right-click menus for
>>      canvas-based feature tracks.  Thanks to Paul Hale for the initial
>>      implementation of this.
>>
>>    * Allow the user to set the document.domain property via jbrowse.conf
>>      which can be helpful especially if jbrowse is embedded in a iframe.
>>      Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix
>>      (issue #440)
>>
>>    * Improved the graphic design of the "Add sequence search" dialog box
>>      to make it clearer how to switch between providing an amino acid
>>      and a nucleotide sequence.  Thanks to Kevin Mohamed for the initial
>>      implementation of this (issue #436).
>>
>>    * Expanded the default color set of `Alignments2` tracks to show
>>      different shades of color indications of reads with missing mate
>>      pairs, improperly aligned reads, and reads with mate pairs on
>>      different reference sequences.  Thanks to Keiran Raine for
>>      implementing this (issue #443).
>>
>>    * Added support to customize specific parts of the 'View details'
>>      popups using callback functions. Thanks to Kieran Raine for the
>>      idea and Colin Diesh for the implementation (issue #421).
>>
>>    * The File->Open tool will now can add files named `*.coverage.*` or
>>      `*.density.*` as histograms to newly-opened tracks if the file
>>      basenames match.  For example, if both `mysample.bam` and
>>      `mysample.coverage.bw` are present, `mysample.coverage.bw` will be
>>      added as a histogram source for `mysample.bam`.  Thanks to Keiran
>>      Raine and Alexander Stoddard for suggesting this (issue #423).
>>
>> ## Bug fixes
>>
>>    * Fixed a problem where the feature arrowhead would get stuck in the
>>      middle of the screen at high zoom levels. Thanks to Colin Diesh for
>>      the fix (issue #449).
>>
>>    * Disabled the FASTA download button in the "View details" page on
>>      Safari (issue #412). This feature can't be supported in Safari at
>>      this time, but it is still supported in most other browsers. Rob
>>      Buels and Colin Diesh contributed fixes to this issue.
>>
>>    * Fixed a bug in the client-side GFF3 parser pointed out by Andrew
>>      Warren.  Thanks Andrew! (issue #452).
>>
>>    * Fixed the problem of translation frames being switched around at
>>      different zoom levels. Thanks to Kieron Taylor for the bug report
>>      and Colin Diesh for the bugfix (issue #435)
>>
>>    * Fixed a bug where gene features in GFF tracks would not have
>>      arrowhead markers. Thanks to Colin Diesh for finding and fixing
>>      this issue (issue #454)
>>
>>
>> Happy browsing.  ;-)
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>>
>>
> ------------------------------------------------------------------------------
> Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually works.
> Faster operations. Version large binaries.  Built-in WAN optimization and the
> freedom to use Git, Perforce or both. Make the move to Perforce.
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Re: JBrowse 1.11.3 released

Robert Buels-2
Thanks Jillian!  It's been a pleasure working with you!

Rob

On 03/09/2014 04:13 AM, Jillian Rowe wrote:
> It's been great watching Jbrowse grow and change this last year. Myself
> and my colleagues truly believe its the best genome browser out there,
> opensource or otherwise.

------------------------------------------------------------------------------
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Re: Histograms with CanvasFeatures in JBrowse

Colin
In reply to this post by TROESSER, DANIEL (AG-Contractor/1000)
Hi Daniel,

I am trying to reproduce the problem and I created an HTMLFeatures track and a CanvasFeatures track and see the histograms being generated from the lf-{Chunk}.json as you described.

I am not sure if this is relevant but I am digging into the code a little bit and I am seeing some things that say that it will only use the pre-generated histogram if it "fits neatly" into the viewport, and there are some TODO items that are saying that we still need to be able to account for finding the right pre-generated histogram (see src/JBrowse/Store/SeqFeature/NCList.js).

So it is possible that choosing the right scale for your pre-generated histograms might help, but it seems that there might be some work to do in this area.

Thanks
-Colin




On Fri, Mar 7, 2014 at 3:59 PM, TROESSER, DANIEL [AG-Contractor/1000] <[hidden email]> wrote:
Does anyone know how to get pre-generated histogram data to work with CanvasFeatures?  We're using LazyNCList files.  It's generating histograms, but it's generating it from the feature data (lf-{Chunk}.json) rather than hist-xxxxxx-{Chunk}.json.

Thanks,

Dan
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subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware".
Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying
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including but not limited to the Export Administration Regulations (EAR) and sanctions regulations issued by the U.S. Department of
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applicable U.S. export laws and regulations.


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Re: Histograms with CanvasFeatures in JBrowse

TROESSER, DANIEL (AG-Contractor/1000)

Hi Colin,

 

Thanks for doing some research on this.  It sounds like I will have to do more experimentation and possibly debugging of the JBrowse code to see how to get this to work.

 

Thanks again,

 

Dan

 

From: Colin [mailto:[hidden email]]
Sent: Monday, March 10, 2014 9:59 AM
To: TROESSER, DANIEL [AG-Contractor/1000]
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Histograms with CanvasFeatures in JBrowse

 

Hi Daniel,


I am trying to reproduce the problem and I created an HTMLFeatures track and a CanvasFeatures track and see the histograms being generated from the lf-{Chunk}.json as you described.

I am not sure if this is relevant but I am digging into the code a little bit and I am seeing some things that say that it will only use the pre-generated histogram if it "fits neatly" into the viewport, and there are some TODO items that are saying that we still need to be able to account for finding the right pre-generated histogram (see src/JBrowse/Store/SeqFeature/NCList.js).

 

So it is possible that choosing the right scale for your pre-generated histograms might help, but it seems that there might be some work to do in this area.

Thanks

-Colin

 

 

 

On Fri, Mar 7, 2014 at 3:59 PM, TROESSER, DANIEL [AG-Contractor/1000] <[hidden email]> wrote:

Does anyone know how to get pre-generated histogram data to work with CanvasFeatures?  We're using LazyNCList files.  It's generating histograms, but it's generating it from the feature data (lf-{Chunk}.json) rather than hist-xxxxxx-{Chunk}.json.

Thanks,

Dan
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Re: JBrowse 1.11.3 released

Andrew Warren
In reply to this post by Robert Buels-2
I would to extend a warm thanks to Robert for his efforts, help, and responsiveness concerning all things JBrowse. Good luck in the future. Job well done.

-Andrew Warren


On Fri, Mar 7, 2014 at 2:27 PM, <[hidden email]> wrote:
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Today's Topics:

   1. JBrowse 1.11.3 released (Robert Buels)
   2. Re: JBrowse 1.11.3 released (Robert Buels)
   3. Re: JBrowse 1.11.3 released (Amelia Ireland)


----------------------------------------------------------------------

Message: 1
Date: Fri, 07 Mar 2014 13:31:22 -0500
From: Robert Buels <[hidden email]>
Subject: [Gmod-ajax] JBrowse 1.11.3 released
To: "[hidden email]"
        <[hidden email]>,      "[hidden email]"
        <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi all,

JBrowse 1.11.3 has been released, with quite a few improvements and
bugfixes, including a new coloring scheme for BAM alignment tracks
(Alignments2 tracks), a fix for some annoying bugs with the feature
arrowheads, and some nice new configuration variables for customizing
the display of certain fields in the default feature detail popup dialog
boxes (see the JBrowse Configuration Guide for details).

It can be downloaded from http://jbrowse.org/jbrowse-1-11-3.

The full release notes:

## Minor improvements

  * Added a "Zoom to this" item in the default right-click menus for
    canvas-based feature tracks.  Thanks to Paul Hale for the initial
    implementation of this.

  * Allow the user to set the document.domain property via jbrowse.conf
    which can be helpful especially if jbrowse is embedded in a iframe.
    Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix
    (issue #440)

  * Improved the graphic design of the "Add sequence search" dialog box
    to make it clearer how to switch between providing an amino acid
    and a nucleotide sequence.  Thanks to Kevin Mohamed for the initial
    implementation of this (issue #436).

  * Expanded the default color set of `Alignments2` tracks to show
    different shades of color indications of reads with missing mate
    pairs, improperly aligned reads, and reads with mate pairs on
    different reference sequences.  Thanks to Keiran Raine for
    implementing this (issue #443).

  * Added support to customize specific parts of the 'View details'
    popups using callback functions. Thanks to Kieran Raine for the
    idea and Colin Diesh for the implementation (issue #421).

  * The File->Open tool will now can add files named `*.coverage.*` or
    `*.density.*` as histograms to newly-opened tracks if the file
    basenames match.  For example, if both `mysample.bam` and
    `mysample.coverage.bw` are present, `mysample.coverage.bw` will be
    added as a histogram source for `mysample.bam`.  Thanks to Keiran
    Raine and Alexander Stoddard for suggesting this (issue #423).

## Bug fixes

  * Fixed a problem where the feature arrowhead would get stuck in the
    middle of the screen at high zoom levels. Thanks to Colin Diesh for
    the fix (issue #449).

  * Disabled the FASTA download button in the "View details" page on
    Safari (issue #412). This feature can't be supported in Safari at
    this time, but it is still supported in most other browsers. Rob
    Buels and Colin Diesh contributed fixes to this issue.

  * Fixed a bug in the client-side GFF3 parser pointed out by Andrew
    Warren.  Thanks Andrew! (issue #452).

  * Fixed the problem of translation frames being switched around at
    different zoom levels. Thanks to Kieron Taylor for the bug report
    and Colin Diesh for the bugfix (issue #435)

  * Fixed a bug where gene features in GFF tracks would not have
    arrowhead markers. Thanks to Colin Diesh for finding and fixing
    this issue (issue #454)


Happy browsing.  ;-)

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org






------------------------------

Message: 2
Date: Fri, 07 Mar 2014 13:36:45 -0500
From: Robert Buels <[hidden email]>
Subject: Re: [Gmod-ajax] JBrowse 1.11.3 released
To: "[hidden email]"
        <[hidden email]>,      "[hidden email]"
        <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi all,

Forgot to mention:

This will be my last JBrowse release in my position as JBrowse lead
developer.

Thank you all for the past two years of development; we?ve made some
exciting strides, and it?s been great working with you!


Robert Buels
Lead Developer (for a few more hours)
JBrowse - http://jbrowse.org

On 03/07/2014 01:31 PM, Robert Buels wrote:
> Hi all,
>
> JBrowse 1.11.3 has been released, with quite a few improvements and
> bugfixes, including a new coloring scheme for BAM alignment tracks
> (Alignments2 tracks), a fix for some annoying bugs with the feature
> arrowheads, and some nice new configuration variables for customizing
> the display of certain fields in the default feature detail popup dialog
> boxes (see the JBrowse Configuration Guide for details).
>
> It can be downloaded from http://jbrowse.org/jbrowse-1-11-3.
>
> The full release notes:
>
> ## Minor improvements
>
>   * Added a "Zoom to this" item in the default right-click menus for
>     canvas-based feature tracks.  Thanks to Paul Hale for the initial
>     implementation of this.
>
>   * Allow the user to set the document.domain property via jbrowse.conf
>     which can be helpful especially if jbrowse is embedded in a iframe.
>     Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix
>     (issue #440)
>
>   * Improved the graphic design of the "Add sequence search" dialog box
>     to make it clearer how to switch between providing an amino acid
>     and a nucleotide sequence.  Thanks to Kevin Mohamed for the initial
>     implementation of this (issue #436).
>
>   * Expanded the default color set of `Alignments2` tracks to show
>     different shades of color indications of reads with missing mate
>     pairs, improperly aligned reads, and reads with mate pairs on
>     different reference sequences.  Thanks to Keiran Raine for
>     implementing this (issue #443).
>
>   * Added support to customize specific parts of the 'View details'
>     popups using callback functions. Thanks to Kieran Raine for the
>     idea and Colin Diesh for the implementation (issue #421).
>
>   * The File->Open tool will now can add files named `*.coverage.*` or
>     `*.density.*` as histograms to newly-opened tracks if the file
>     basenames match.  For example, if both `mysample.bam` and
>     `mysample.coverage.bw` are present, `mysample.coverage.bw` will be
>     added as a histogram source for `mysample.bam`.  Thanks to Keiran
>     Raine and Alexander Stoddard for suggesting this (issue #423).
>
> ## Bug fixes
>
>   * Fixed a problem where the feature arrowhead would get stuck in the
>     middle of the screen at high zoom levels. Thanks to Colin Diesh for
>     the fix (issue #449).
>
>   * Disabled the FASTA download button in the "View details" page on
>     Safari (issue #412). This feature can't be supported in Safari at
>     this time, but it is still supported in most other browsers. Rob
>     Buels and Colin Diesh contributed fixes to this issue.
>
>   * Fixed a bug in the client-side GFF3 parser pointed out by Andrew
>     Warren.  Thanks Andrew! (issue #452).
>
>   * Fixed the problem of translation frames being switched around at
>     different zoom levels. Thanks to Kieron Taylor for the bug report
>     and Colin Diesh for the bugfix (issue #435)
>
>   * Fixed a bug where gene features in GFF tracks would not have
>     arrowhead markers. Thanks to Colin Diesh for finding and fixing
>     this issue (issue #454)
>
>
> Happy browsing.  ;-)
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
>
>



------------------------------

Message: 3
Date: Fri, 7 Mar 2014 11:26:27 -0800
From: Amelia Ireland <[hidden email]>
Subject: Re: [Gmod-ajax] JBrowse 1.11.3 released
To: Robert Buels <[hidden email]>
Cc: "[hidden email]"
        <[hidden email]>
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

Thank you Rob for making such fantastic progress, and for your tireless
devotion to JBrowse and GMOD. On behalf of GMOD, all the very best for the
future, and thank you for your hard work!

Amelia
GMOD Community Support


On Fri, Mar 7, 2014 at 10:36 AM, Robert Buels <[hidden email]> wrote:

> Hi all,
>
> Forgot to mention:
>
> This will be my last JBrowse release in my position as JBrowse lead
> developer.
>
> Thank you all for the past two years of development; we've made some
> exciting strides, and it's been great working with you!
>
>
> Robert Buels
> Lead Developer (for a few more hours)
> JBrowse - http://jbrowse.org
>
> On 03/07/2014 01:31 PM, Robert Buels wrote:
> > Hi all,
> >
> > JBrowse 1.11.3 has been released, with quite a few improvements and
> > bugfixes, including a new coloring scheme for BAM alignment tracks
> > (Alignments2 tracks), a fix for some annoying bugs with the feature
> > arrowheads, and some nice new configuration variables for customizing
> > the display of certain fields in the default feature detail popup dialog
> > boxes (see the JBrowse Configuration Guide for details).
> >
> > It can be downloaded from http://jbrowse.org/jbrowse-1-11-3.
> >
> > The full release notes:
> >
> > ## Minor improvements
> >
> >   * Added a "Zoom to this" item in the default right-click menus for
> >     canvas-based feature tracks.  Thanks to Paul Hale for the initial
> >     implementation of this.
> >
> >   * Allow the user to set the document.domain property via jbrowse.conf
> >     which can be helpful especially if jbrowse is embedded in a iframe.
> >     Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix
> >     (issue #440)
> >
> >   * Improved the graphic design of the "Add sequence search" dialog box
> >     to make it clearer how to switch between providing an amino acid
> >     and a nucleotide sequence.  Thanks to Kevin Mohamed for the initial
> >     implementation of this (issue #436).
> >
> >   * Expanded the default color set of `Alignments2` tracks to show
> >     different shades of color indications of reads with missing mate
> >     pairs, improperly aligned reads, and reads with mate pairs on
> >     different reference sequences.  Thanks to Keiran Raine for
> >     implementing this (issue #443).
> >
> >   * Added support to customize specific parts of the 'View details'
> >     popups using callback functions. Thanks to Kieran Raine for the
> >     idea and Colin Diesh for the implementation (issue #421).
> >
> >   * The File->Open tool will now can add files named `*.coverage.*` or
> >     `*.density.*` as histograms to newly-opened tracks if the file
> >     basenames match.  For example, if both `mysample.bam` and
> >     `mysample.coverage.bw` are present, `mysample.coverage.bw` will be
> >     added as a histogram source for `mysample.bam`.  Thanks to Keiran
> >     Raine and Alexander Stoddard for suggesting this (issue #423).
> >
> > ## Bug fixes
> >
> >   * Fixed a problem where the feature arrowhead would get stuck in the
> >     middle of the screen at high zoom levels. Thanks to Colin Diesh for
> >     the fix (issue #449).
> >
> >   * Disabled the FASTA download button in the "View details" page on
> >     Safari (issue #412). This feature can't be supported in Safari at
> >     this time, but it is still supported in most other browsers. Rob
> >     Buels and Colin Diesh contributed fixes to this issue.
> >
> >   * Fixed a bug in the client-side GFF3 parser pointed out by Andrew
> >     Warren.  Thanks Andrew! (issue #452).
> >
> >   * Fixed the problem of translation frames being switched around at
> >     different zoom levels. Thanks to Kieron Taylor for the bug report
> >     and Colin Diesh for the bugfix (issue #435)
> >
> >   * Fixed a bug where gene features in GFF tracks would not have
> >     arrowhead markers. Thanks to Colin Diesh for finding and fixing
> >     this issue (issue #454)
> >
> >
> > Happy browsing.  ;-)
> >
> > Robert Buels
> > Lead Developer
> > JBrowse - http://jbrowse.org
> >
> >
> >
>
>
> ------------------------------------------------------------------------------
> Subversion Kills Productivity. Get off Subversion & Make the Move to
> Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually works.
> Faster operations. Version large binaries.  Built-in WAN optimization and
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> freedom to use Git, Perforce or both. Make the move to Perforce.
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> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>



--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject
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Re: Histograms with CanvasFeatures in JBrowse

Colin
In reply to this post by TROESSER, DANIEL (AG-Contractor/1000)
Hi Daniel,
Did you ever find any solution to your problem here? In any case, I think generating histograms should definitely be clarified, but I just wanted to check to see if you had any luck with your case.
Thanks,
-Colin


On Mon, Mar 10, 2014 at 12:16 PM, TROESSER, DANIEL [AG-Contractor/1000] <[hidden email]> wrote:

Hi Colin,

 

Thanks for doing some research on this.  It sounds like I will have to do more experimentation and possibly debugging of the JBrowse code to see how to get this to work.

 

Thanks again,

 

Dan

 

From: Colin [mailto:[hidden email]]
Sent: Monday, March 10, 2014 9:59 AM
To: TROESSER, DANIEL [AG-Contractor/1000]
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Histograms with CanvasFeatures in JBrowse

 

Hi Daniel,


I am trying to reproduce the problem and I created an HTMLFeatures track and a CanvasFeatures track and see the histograms being generated from the lf-{Chunk}.json as you described.

I am not sure if this is relevant but I am digging into the code a little bit and I am seeing some things that say that it will only use the pre-generated histogram if it "fits neatly" into the viewport, and there are some TODO items that are saying that we still need to be able to account for finding the right pre-generated histogram (see src/JBrowse/Store/SeqFeature/NCList.js).

 

So it is possible that choosing the right scale for your pre-generated histograms might help, but it seems that there might be some work to do in this area.

Thanks

-Colin

 

 

 

On Fri, Mar 7, 2014 at 3:59 PM, TROESSER, DANIEL [AG-Contractor/1000] <[hidden email]> wrote:

Does anyone know how to get pre-generated histogram data to work with CanvasFeatures?  We're using LazyNCList files.  It's generating histograms, but it's generating it from the feature data (lf-{Chunk}.json) rather than hist-xxxxxx-{Chunk}.json.

Thanks,

Dan
This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled
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all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.

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The information contained in this email may be subject to the export control laws and regulations of the United States, potentially
including but not limited to the Export Administration Regulations (EAR) and sanctions regulations issued by the U.S. Department of
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applicable U.S. export laws and regulations.


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Re: Histograms with CanvasFeatures in JBrowse

Colin
We took some steps to resolve this issue in the latest release of JBrowse (1.11.4). The fix only requires a simple config change (set
histograms.binsPerBlock=25)
, so you can apply this to tracks on older versions of JBrowse if you see this problem. Please see https://github.com/GMOD/jbrowse/issues/475 for details

Thanks again for reporting the issue
-Colin


On Tue, Mar 25, 2014 at 1:37 PM, Colin <[hidden email]> wrote:
Hi Daniel,
Did you ever find any solution to your problem here? In any case, I think generating histograms should definitely be clarified, but I just wanted to check to see if you had any luck with your case.
Thanks,
-Colin


On Mon, Mar 10, 2014 at 12:16 PM, TROESSER, DANIEL [AG-Contractor/1000] <[hidden email]> wrote:

Hi Colin,

 

Thanks for doing some research on this.  It sounds like I will have to do more experimentation and possibly debugging of the JBrowse code to see how to get this to work.

 

Thanks again,

 

Dan

 

From: Colin [mailto:[hidden email]]
Sent: Monday, March 10, 2014 9:59 AM
To: TROESSER, DANIEL [AG-Contractor/1000]
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Histograms with CanvasFeatures in JBrowse

 

Hi Daniel,


I am trying to reproduce the problem and I created an HTMLFeatures track and a CanvasFeatures track and see the histograms being generated from the lf-{Chunk}.json as you described.

I am not sure if this is relevant but I am digging into the code a little bit and I am seeing some things that say that it will only use the pre-generated histogram if it "fits neatly" into the viewport, and there are some TODO items that are saying that we still need to be able to account for finding the right pre-generated histogram (see src/JBrowse/Store/SeqFeature/NCList.js).

 

So it is possible that choosing the right scale for your pre-generated histograms might help, but it seems that there might be some work to do in this area.

Thanks

-Colin

 

 

 

On Fri, Mar 7, 2014 at 3:59 PM, TROESSER, DANIEL [AG-Contractor/1000] <[hidden email]> wrote:

Does anyone know how to get pre-generated histogram data to work with CanvasFeatures?  We're using LazyNCList files.  It's generating histograms, but it's generating it from the feature data (lf-{Chunk}.json) rather than hist-xxxxxx-{Chunk}.json.

Thanks,

Dan
This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled
to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and
all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.

All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its
subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware".
Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying
this e-mail or any attachment.


The information contained in this email may be subject to the export control laws and regulations of the United States, potentially
including but not limited to the Export Administration Regulations (EAR) and sanctions regulations issued by the U.S. Department of
Treasury, Office of Foreign Asset Controls (OFAC).  As a recipient of this information you are obligated to comply with all
applicable U.S. export laws and regulations.


------------------------------------------------------------------------------
Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works.
Faster operations. Version large binaries.  Built-in WAN optimization and the
freedom to use Git, Perforce or both. Make the move to Perforce.
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Re: Histograms with CanvasFeatures in JBrowse

TROESSER, DANIEL (AG-Contractor/1000)

Great!  Thanks Colin!  We will try this when we get a chance.  I just now saw your previous follow up on Mar. 25.  I was on vacation at that time and your email got lost in a flood of others.

 

Thanks again,

 

Dan

 

From: Colin [mailto:[hidden email]]
Sent: Monday, May 19, 2014 4:45 PM
To: TROESSER, DANIEL [AG-Contractor/1000]
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Histograms with CanvasFeatures in JBrowse

 

We took some steps to resolve this issue in the latest release of JBrowse (1.11.4). The fix only requires a simple config change (set

histograms.binsPerBlock=25)

, so you can apply this to tracks on older versions of JBrowse if you see this problem. Please see https://github.com/GMOD/jbrowse/issues/475 for details

Thanks again for reporting the issue

-Colin

 

On Tue, Mar 25, 2014 at 1:37 PM, Colin <[hidden email]> wrote:

Hi Daniel,
Did you ever find any solution to your problem here? In any case, I think generating histograms should definitely be clarified, but I just wanted to check to see if you had any luck with your case.

Thanks,

-Colin

 

On Mon, Mar 10, 2014 at 12:16 PM, TROESSER, DANIEL [AG-Contractor/1000] <[hidden email]> wrote:

Hi Colin,

 

Thanks for doing some research on this.  It sounds like I will have to do more experimentation and possibly debugging of the JBrowse code to see how to get this to work.

 

Thanks again,

 

Dan

 

From: Colin [mailto:[hidden email]]
Sent: Monday, March 10, 2014 9:59 AM
To: TROESSER, DANIEL [AG-Contractor/1000]
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Histograms with CanvasFeatures in JBrowse

 

Hi Daniel,


I am trying to reproduce the problem and I created an HTMLFeatures track and a CanvasFeatures track and see the histograms being generated from the lf-{Chunk}.json as you described.

I am not sure if this is relevant but I am digging into the code a little bit and I am seeing some things that say that it will only use the pre-generated histogram if it "fits neatly" into the viewport, and there are some TODO items that are saying that we still need to be able to account for finding the right pre-generated histogram (see src/JBrowse/Store/SeqFeature/NCList.js).

 

So it is possible that choosing the right scale for your pre-generated histograms might help, but it seems that there might be some work to do in this area.

Thanks

-Colin

 

 

 

On Fri, Mar 7, 2014 at 3:59 PM, TROESSER, DANIEL [AG-Contractor/1000] <[hidden email]> wrote:

Does anyone know how to get pre-generated histogram data to work with CanvasFeatures?  We're using LazyNCList files.  It's generating histograms, but it's generating it from the feature data (lf-{Chunk}.json) rather than hist-xxxxxx-{Chunk}.json.

Thanks,

Dan
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