JBrowse-1.11.6 maintenance release

I’m pleased to announce JBrowse 1.11.6 is now available! Everybody’s feedback, bug reports, pull requests, and feature requests have been invaluable for making this happen. This release includes new UI options for easily setting “Log scale” on wiggle tracks and dynamically changing strandedness on RNA-seq according to multi-segment template flags and splice site (XS) flags. It also includes bug fixes for calculating SNP positions on certain flag combinations in BAM files and for reporting the correct genotypes on certain VCF tracks. Enjoy!

Minor improvements

  • Added the ability to customize the contents of HTMLFeatures and CanvasFeatures mouseover tooltips more extensively. Thanks to David Muller for the original bug report and Colin Diesh for the fix (issue #480).
  • Added new options for BigWig files to use min/max summary values when zoomed out using scoreType. Thanks to Scott Cain for reporting the issue and to Colin Diesh for the fix (issue #518).
  • Added a checkbox for wiggle type tracks to have log scale. Thanks to Han Lin for the pull request (issue #502).
  • Added the ability to display paired-end reads in the same direction on Alignments2 tracks with the “Use reverse template” option. Thanks to Tomaz Berisa and Colin Diesh for their contributions (issue #485).
  • Added the ability to parse boolean literals from the .conf files.
  • Added the ability to specify a codon table (or partial codon table) for the Sequence track.
  • Added the ability to show or hide the main menu bar using the configuration file.

Bug fixes

  • Fixed “boolean is not a function” error when using CanvasFeatures tracks with the Segments glyph in some situations.
  • Fixed a dialog box display issue for VCF variants with “no call” specified (issue #513).
  • Fixed loading files from certain filepaths with special characters. Thanks to Ben Bimber for reporting and helping diagnose the bug (issue #508).
  • Fixed popup-dialog callbacks not being called on BAM Alignments tracks in 1.11.5.
  • Fixed systemwide installations of JBrowse perl modules when using Module::Build.
  • Fixed a bug when displaying SNPs on hard clipped reads. Thanks to Thon de Boer for the bug report and to Colin Diesh for the fix (issue #516).
  • Fixed a bug when displaying SNPs on spliced alignments. Thanks to GitHub user 09140930 for the bug report and to Colin Diesh for the fix (issue #523).
  • Fixed a bug that affected some VCF and GFF popup dialogs in some browsers, particularly Chrome 38 (issue #522).
  • Fixed a bug with the incremental indexing with generate-names that associated the wrong track with the name store. Thanks to Richard Hayes for reporting this issue and to Colin Diesh for the fix (issue #526).
  • Fixed the --workdir parameter in generate-names.pl (issue #506).
  • Fixed the display of alternative alleles in the genotype for VCF pop-ups (issue #533).
  • Fixed an issue where some paired-end read data wouldn’t display properly if they had the same start position (issue #521).
  • Output .htaccess file for generate-names.pl when using the compress option. Thanks to Sebastien Carrere for reporting the bug (issue #541).
  • Fixed a small bug with being able to scroll past end of chromosome when using the --sizes option to prepare-refseqs.pl (issue #535).
  • Fixed a small internal code inconsistency with the positioning of the vertical position line. Thanks to Anurag Priyam for the fix (issue #545).
  • Fixed a small bug with some stylesheets not being able to be used for the CanvasFeatures coloring, for example, LESS stylesheets. Thanks to Anurag Priyam for reporting the issue (issue #527).
  • Fixed a small bug with mouseovers on Wiggle type tracks. Thanks to Han Lin for finding and fixing this bug (issue #503).
  • Removed XS tag from the strand calculation for alignments and made it an optional rendering option for BAM files with the “Use XS” option. Thanks to Kieran Raine and the pull request (issue #473).
  • Added a bugfix that prevented viewing the details of haploid VCF files. Thanks to Colin Diesh for finding and fixing this bug (issue #536).
  • Added a bugfix for an issue that made browsing very buggy when using private browsing mode in Safari.
  • Fixed the shortDescription option for the mouseover description of tracks in the Hierarchical track list (issue #553).
  • Re-added filter options that were missing for SNPCoverage tracks.
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JBrowse-1.11.5 maintenance release

A new JBrowse release has arrived! JBrowse 1.11.5 incorporates many valuable contributions and feedback from the community which has been overwhelmingly positive. Some notable bugs have been fixed, including a long-standing VCF file parsing bug, a scrolling bug that affected popup boxes for variants on JBrowse 1.11.4, and a patch for setup.sh build errors. There are also some new configuration options for the tracklist and dialog boxes, and the ability to use tablet and touch-screen devices has been fixed!

Minor improvements

  • Added the ability to disable sorting on the Hierarchical track selector using the sortHierarchical flag. Thanks to Chris Childers for the suggestion and Colin Diesh for the implementation (issue #477).
  • Added saving of the display mode setting on the CanvasFeature based tracks. Thanks to Jon Hinton for the idea and Colin Diesh for the fix (issue #469).
  • Added configurable click event handlers for Wiggle type tracks. Thanks to Richard Hayes for implementing this feature (issue #489).
  • Added more configuration options for ‘View details’ popups as well as the ability to customize the ‘About track’ popups. Thanks to Colin Diesh for the idea and implementation (issue #494).
  • Added the ability to load the category attribute from trackMetaData files to be used for the Hierarchical track selector.
  • Added the ability to specify initially collapsed categories in the Hierarchical track selector (issue #507).
  • Added beta touch-screen and tablet support by fixing a related bug. Thanks to Paul Hale and Kieran Raine for reporting bugs and to Emily Greenfest-Allen for the suggested fix (issue #505).

Bug fixes

  • Fixed a bug with VCF tabix file parsing that caused unnecessary chunkSizeLimit errors. Thanks to Richard Hayes for finding and debugging this issue (issue #486)!
  • Fixed a bug where the Variant popup boxes would not display complete genotype information in previous 1.11.* versions. Thanks to Nando for reporting the bug and Colin Diesh for the bugfix (issue #488).
  • Fixed a small error that occured when using variant type tracks with the REST API.
  • Added a bugfix that caused problems scrolling in dialog boxes for variant type tracks in 1.11.4 (issue #492).
  • Fixed the use of the –refs flag on prepare-refseqs.pl. Thanks to Audrey for finding & fixing this bug (issue #497).
  • Added missing template length flag to the Alignments popup dialogs. Thanks to Kieran Raine for the suggestion and Colin Diesh for the fix (issue #471).
  • Fixed the functionality of the –incremental flag in the generate-names.pl script. Thanks to Richard Hayes and Colin Diesh fixing the issue (issue #478).
  • Fixed legacy bam-to-json.pl support when running setup.sh due to samtools build modifications (issue #501).
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JBrowse-1.11.4 maintenance release

I am happy to announce the release of JBrowse 1.11.4. This is the first release after Rob’s leave, and it represents the great community effort to keep things going. There are some exciting new developments in this version, including high-resolution rendering of canvas-based tracks and a basic GTF file parser. There are also several important bug fixes, including an update to the setup.sh script in order to maintain compatibility with the latest BioPerl.

Minor improvements

  • Added high-resolution rendering for CanvasFeatures, SNPCoverage, BigWig tracks, and histograms. This allows rendering for canvas- based tracks to look much sharper on high-resolution displays and can even look sharper when zooming. The high-resolution rendering is disabled by default to avoid conflicts with existing instances, but feel free to test it out by setting “highResolutionMode” in jbrowse.conf. Thanks to Colin Diesh for the idea and implementation (issue #456)
  • Added the ability to run jbrowse scripts outside of the JBrowse root directory. Thanks to Chien-Chi Lo for the patch (issue #465).
  • Added basic GTF parser that can open files from the File->Open menu or by using the in-memory adaptor. Big thanks to Andrew Warren for the contribution (issue #453).
  • Added a change to the highlight button to allow the user to more easily clear highlights. Thanks to Paul Hale for the suggestion and Colin Diesh for the fix (issue #445).

Bug fixes

  • Fixed help page icons not loading since JBrowse 1.11.2. Thanks to Colin Diesh for catching the bug and fixing it (issue #460).
  • Fixed updating of the y-axis scale when using the resize quantitative tracks feature. Thanks again to Evan Briones for the original implementation and Colin Diesh for the fix (issue #461).
  • Changed the CanvasFeatures ‘View details’ pages to display the name and description of features in the dialog box. Thanks to Colin Diesh for the fix (issue #463).
  • Added a bugfix for non-compliant servers that add a trailing slash to the URL. Thanks to Colin Diesh for the fix (issue #462).
  • Fixed a broken link in the documentation for biodb-to-json.
  • Updated setup.sh to maintain compatibility with the latest BioPerl. Thanks to Thomas Sibley and Scott Cain for helping with this issue (issue #468).
  • Fixed a long standing bug with the coloring of nucleotides on the SNPCoverage/Alignments2 track. Thanks to Long Le for reporting this on the mailing list.
  • Fixed a long standing bug with the scrollbar in the dialog box on Chrome and Safari browsers. Thanks to the #dojo irc channel and and Colin Diesh for helping fix this problem (issue #386).
  • Fix a small rendering problem that causes one pixel gap to appear on Safari due to subpixel rendering issues. Thanks to Colin Diesh for the preliminary fix (issue #341).
  • Fix a bug with CanvasFeatures based tracks loading huge amounts of data to generate histograms instead of using pre-generated histograms. Thanks to Daniel Troesser for reporting this on the mailing list and Colin Diesh for the fix (issue #475).

 

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JBrowse 1.11.3 maintenance release

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).

In addition, 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!

Files for download:

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)
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Tutorial: exploring structural variation using JBrowse, from the tomato 150+ re-seq project

We recently used JBrowse in the 150 Tomato Genome ReSequencing project, and it worked great!

The aim of the 150 Tomato Genome ReSequencing project (http://www.tomatogenome.net) is to reveal and explore the genetic variation available in tomato. Tomato has been selected as target crop because it is economically one of the most important crop species for the Dutch breeding industry, and is one the most important vegetables globally. However, since the tomato shows only limited genetic diversity in commercial breeding lines, valuable alleles will be available in wild tomato relatives. Since breeding and selection was targeted at only a narrow range of desirable agricultural traits, also old breeding material could be source of interesting alleles that have been lost during domestication.

In order to identify the sequence diversity within tomato, 83 genotypes including 10 old varieties, 43 land races and 30 wild accessions were seqeunced. These wild tomato species represent the full range of expected genetic variation around S. lycopersicum that can still be used as potential breeding material.

Sequences have been mapped against the reference genome of S. lycopersicum cv. Heinz (SL2.40) and SNP and INDEL variation has been determined.

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl.

The SNP and INDEL variants have been made available using JBowse (http://www.tomatogenome.net/VariantBrowser/) and an tutorial (http://gmod.org/wiki/JBrowse#Tutorials) on how to explore this data resource by the community has been written.

In addition to variants from the 150+ Tomato Genome ReSequencing project, we will add publicly available variant datasets as well.

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JBrowse 1.11.2 maintenance release

JBrowse 1.11.2 has been released, with some new controls to adjust the size of quantitative tracks (thanks to Evan Briones at University of Arizona!), added support for the new text-based tracks.conf files to generate-names.pl, and quite a few other small improvements.

Files for download:

Minor improvements

  • Added some user interface elements to set the height in pixels of a
    single quantitative track, or of all visible quantitative tracks.
    Thanks to Evan Briones for implementing this!
  • Added a JBrowse/View/FeatureGlyph/Diamond glyph that draws
    diamond-shaped features instead of boxes. Thanks to OICR Co-op
    student Kevin Mohamed for implementing this!
  • Reference sequence tracks now display a “no sequence” message
    instead of a bunch of blank blocks when the reference sequence
    basepairs aren’t available. Thanks to Kevin Mohamed for
    implementing this (issue #422).
  • Persistent session state is now stored on a per-dataset basis,
    which improves user experience when switching between multiple
    datasets in JBrowse. Thanks to Richard Hayes for pointing this
    issue out, and Kevin Mohamed for the fix (issue #410).
  • “Hide sites not passing …” settings in VCF track menus now show
    the filter’s long description when hovered over. Thanks to Keiran
    Raine for suggesting this (issue #420).
  • Tweaked display of track labels and added a slight border at the
    top edge of each track to make it more clear which track data
    belongs to. Thanks to Keiran Raine for suggesting this, and Kevin
    Mohamed for the initial implementation (issue #432).
  • Added a --config option to flatfile-to-json.pl that accepts
    additional configuration variables that will be merged into the top
    level of the track configuration. Thanks to Mikael Brandström
    Durling for the initial implementation of this.

Bug fixes

  • generate-names.pl now indexes VCF files from track definitions in
    tracks.conf files. Thanks to Paul Halle for pointing this out
    (issue #434).
  • Added a missing dependency for the server side formatting tools on
    List::MoreUtil 0.28 or higher. Thanks to Cris Lawrence and Keiran
    Raine for troubleshooting this!
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JBrowse 1.11.1 maintenance release

JBrowse 1.11.1 has been released, with a number of bug fixes and some nice improvements to Alignments2 tracks. Most of the Alignments2 improvements were thought up by Keiran Raine at Sanger, thanks Keiran! Thanks also to Cris Lawrence and Richard Hayes, who were helpful in finding some other bugs and opportunities for improvements.

Files for download:

Minor improvements

  • Alignments2 tracks now include right-click menu items to view the
    location of an alignment’s mate pair or next segment in a popup or
    a new tab. Thanks to Keiran Raine for suggesting this (issue #406).

  • Alignments2 tracks now draw gaps and deletions in reads regardless
    of zoom level, as long as the alignment is at least 3 pixels wide
    in the display. Thanks to Keiran Raine for pointing out the need
    for this (issue #403).

  • Added support for a histograms.max variable for
    CanvasFeatures-based tracks that can be used to manually set the
    max value of a histogram display. Thanks to Keiran Raine for
    pointing out the need for this.

  • Added support for drawing clip markers (with their color set by
    histograms.clip_marker_color) in CanvasFeatures-based
    tracks. Thanks to Keiran Raine for pointing out the need for this
    (issue #402).

  • Canvas-based feature tracks now try to draw histograms, if
    available, when the data backend throws a data-overflow error (like
    when the BAM backend exceeds the chunkSizeLimit). Thanks to Keiran
    Raine for motivating this (issue #405).

  • Make it easier to set JS loading baseUrl by moving it into the
    initial dojo configuration. Thanks to Jillian Rowe for pointing
    out the need for this.

  • Enhanced new text-based config syntax to support arrays of values
    in a list like:

    [trackMetadata]
    sources =
      + data/mymeta.csv
      + data/more_meta.csv
    

Bug fixes

  • When a number is typed into the location box, JBrowse first checks
    if it is the name of a feature in the names index, and only
    interprets it as a coordinate if it is not found in the names
    index. Thanks to Richard Hayes for pointing this out (issue #407).

  • Fixed bug that caused client-side GFF3 tracks to appear as
    “Loading” forever if the GFF3 is malformed (like malformed GFF3
    files that are opened with the File->Open tool).

  • Fixed bug in which no default value for
    maxFeatureSizeForUnderlyingRefSeq was being set, which made
    default feature detail popups try to fetch and display a feature’s
    underlying reference sequence even if it is way too large, unless
    the variable was set explicitly in the configuration.

  • JBrowse now shows a more understandable error message when trying
    to open an uncompressed BAM file. Thanks to Keiran Raine for
    pointing this out (issue #404).

  • Fixed jbrowse.conf faceted track selector configuration examples
    not working as written. Thanks to Cris Lawrence for pointing this
    out.

  • Fixed a bug in which right-clicking on feature labels in an
    HTMLFeatures-based track did not bring up the right-click menu for
    a feature. Thanks to Cris Lawrence for pointing this out (issue #408).

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JBrowse 1.11.0: hierarchical track selector, easier configuration, summary mode

JBrowse 1.11.0 is out today, with some major new features, and, as always, quite a lot of smaller bugfixes and improvements.

But first, the download links:

Firstly, JBrowse has added a third track selector type alongside the existing Simple (small) and Faceted (large) track selectors called Hierarchical.  It looks like the old Simple track selector (which was the default), except it pays attention to the “category” key in a track’s metadata, and if it is present, it organizes the tracks into nested, collapsible panes based on that.  Also, instead of the drag-and-drop paradigm used by the Simple track selector, the Hierarchical track selector turns tracks on and off by just checking and unchecking the box next to each track.  I think the checkboxes are probably easier for new users to understand, as well, the Hierarchical track selector is now enabled by default.  Those that prefer the old Simple selector can always turn it on by setting trackSelector.type to “Simple” in the jbrowse_conf.json file or the new jbrowse.conf file, which brings me to my next item.

Secondly, JBrowse now has a additional text configuration format that is designed to be easier to hand edit, and can coexist and interoperate with existing JSON configuration files.  Users of GBrowse will find the syntax very familiar, since its design borrows heavily from GBrowse’s configuration syntax.  Here’s a side-by-side comparison of what you would write in the old JSON and new text configuration formats to make JBrowse use the old Simple track selector.

jbrowse_conf.json jbrowse.conf
"trackSelector": {
  "type": "Simple"
}
[trackSelector]
type = Simple

It’s easier to configure tracks in the new format, as well.  Here’s a typical BAM Alignments2 track configuration in both formats, for comparison.

trackList.json
"tracks": [
  {
    "storeClass"  : "JBrowse/Store/SeqFeature/BAM",
    "urlTemplate" : "../../raw/volvox/volvox-sorted.bam",
    "label"       : "volvox-sorted-bam",
    "type"        : "JBrowse/View/Track/Alignments2",
    "key"         : "My BAM track"
  }
]
tracks.conf
[tracks.volvox-sorted-bam]
storeClass  = JBrowse/Store/SeqFeature/BAM
urlTemplate = ../../raw/volvox/volvox-sorted.bam
type        = JBrowse/View/Track/Alignments2
key         = My BAM track

And for the final headline feature of this release, JBrowse CanvasFeatures, CanvasVariants, and Alignments2 tracks can now be configured to show feature density histograms or coverage plots when zoomed too far out to display individual features.  They can take this quantitative data from any type of JBrowse data store (including REST stores), but most users would want to use a BigWig store.    One caveat: this isn’t a full-featured quantitative display like a Wiggle/XYPlot track, so quantitative values need to all be greater than 0, and all you can really change about how it looks is its color.  Here’s an example in the new text configuration syntax of an Alignments2 track that will display either alignments from a BAM file or a coverage plot from a BigWig file, depending on zoom level.

[tracks.my-bam-with-coverage]

storeClass  = JBrowse/Store/SeqFeature/BAM
urlTemplate = my_alignments.bam

type        = JBrowse/View/Track/Alignments2
key         = My BAM track

histograms.storeClass = JBrowse/Store/SeqFeature/BigWig
histograms.urlTemplate = my_alignments.bam.coverage.bw
histograms.description = coverage plot
histograms.color = #dcdcdc

Of course, there are many smaller improvements and bug fixes.  Read on for the complete release notes.

Release 1.11.0

Major improvements

  • Introduced density/coverage histogram support for CanvasFeatures,
    CanvasVariants, and Alignments2 tracks. These track types now
    support an optional histograms configuration subsection that can
    contain a definition for a second datastore that holds quantitative
    data (usually either coverage depth or feature density) to be
    displayed when zoomed further out than featureScale (or if
    featureScale is not set, the scale determined by the store’s
    feature density divided by maxFeatureScreenDensity). Thanks to
    Richard Hayes for pushing hard for this feature.
  • Added a new “Hierarchical” track selector that shows tracks in a
    hierarchy of collapsible categories, which is now the default track
    selector. To assign categories and subcategories to your tracks,
    set category or metadata.category attributes on each configured
    tracks in your trackList.json. Thanks to the many users who have
    requested this at one time or another.
  • JBrowse now supports a new plaintext configuration format that
    users of GBrowse will find very familiar, since it is designed to
    be very similar to it. This syntax is also much easier to
    hand-write than JSON. The JSON configuration syntax is not going
    away, and will continue to be supported.

    Thanks to Erik Derohanian for the original implementation of this
    configuration adaptor, and Richard Hayes and Keiran Raine for
    motivating the work to polish and more fully integrate it.

  • Variables in configuration files can now be based on the contents
    of other variables. For example, setting

    “myCustomVariable”: “/some/custom/path”,
    “include”: “{myCustomVariable}/conf.json”

    will try to include a configuration file located at
    “/some/custom/path/conf.json”. Interpolation is done as the final
    step in configuration loading, so variables can come from anywhere
    in the configuration.

  • When JBrowse is started, if there are no reference sequences found
    in the default dataRoot, but the dataset selector is configured,
    JBrowse shows a simple list of links to available datasets instead
    of the “Congratulations, JBrowse is on the web” page. Thanks to
    Saulo Aflitos for the idea and its initial implementation.
  • For users wishing to convert existing JSON configuration files to
    the new format, there is a new script, bin/json2conf.pl, that
    does a fair job. Run bin/json2conf.pl -? for details on how to
    use it.
  • Added a new REST backend for name lookup and autocompletion. See
    http://gmod.org/wiki/JBrowse_Configuration_Guide#JBrowse_REST_Names_API
    for details. Thanks to Erik Derohanian for implementing this, and
    Ben Booth for suggesting an API design (issue #267).
  • Major performance and scalability improvements for
    generate-names.pl. Now uses a different algorithm that is faster
    and more scalable than before, and no longer relies on BerkeleyDB
    for temporary storage. This should also alleviate the need to run
    generate-names.pl with --safeMode in Perl 5.10 and earlier. In
    fact, the --safeMode argument to generate-names.pl no longer has
    any effect. Thanks to Cris Lawrence for pointing out the
    continuing need for more scalability.

Minor improvements

  • Detail popups for CanvasVariants and HTMLVariants tracks now
    display the reference sequence itself instead of just “ref” in
    genotype displays. Thanks to Cris Lawrence for requesting this.
  • Added a “save as FASTA” button to default feature detail popups
    that downloads a FASTA file with the displayed piece of reference
    sequence (issue #299).
  • chunkSizeLimit for VCF files now defaults to 1 MiB. It used to
    be 15 MiB, which was really far too big for browsers to handle.
  • Added support for a --nameAttributes argument to
    flatfile-to-json.pl that takes a comma-separated list of feature
    attributes to index for name searching and completions, or ‘none’
    to not make names searchable.
  • Added support for a nameAttributes variable in biodb-to-json.pl
    track configurations that can be set to an array of feature
    attribute names to to index for name searching and completions, or
    ‘none’ to not make names searchable.
  • Add a --category argument to bin/wig-to-json.pl that can be used
    to set the metadata.category of a track.

Bug fixes

  • Fixed a bug in NCList data backed in which feature histograms were
    often calculated very incorrectly.
  • Fixed a bug in the VCF data backend that caused not all VCF
    features to be shown in some files at some zoom levels.
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JBrowse 1.10.12 maintenance release (please upgrade!)

JBrowse 1.10.12 has been released, and we are asking all users of JBrowse 1.10.7 1.10.10 and higher to please upgrade to this release as soon as possible.

The story behind this is a bit embarassing: I discovered today that JBrowse releases 1.10.7 through 1.10.10 and 1.10.11 shipped with usage analytics reporting disabled. This is a little piece of code that tracks how many installations and users of JBrowse there are, and the data it provides is absolutely crucial for the JBrowse project, because we use it to try to convince funding agencies that JBrowse is a project worth funding.

So, yes … this release has analytics reporting re-enabled. There are also a few other minor improvements and bug fixes. Please upgrade to this ASAP if you are using JBrowse 1.10.7, 1.10.8, 1.10.9,  1.10.10 or 1.10.11, because we really need that analytics data.

Edit (Dec 11): realized just now that only 1.10.10 and 1.10.11 were affected.  Forgot to account for branching and merging last night.

Files for download:

Minor improvements

  • bam-to-json.pl and flatfile-to-json.pl now support a
    --metadata argument that can add a metadata stanza to track
    configurations they generate.
  • Multi-valued attributes in default feature detail popups are
    displayed as a string of boxes, each containing a value, to avoid
    misinterpretation. Thanks to Cris Lawrence for pointing out the
    need for this.

Bug fixes

  • Re-enabled usage analytics reporting, which had been disabled by a
    stray piece of debugging code since the 1.10.7 release.
  • Fixed a bug in which the tooltip in canvas-based feature tracks
    would sometimes display incorrect label or description text.
Posted in Development, Software releases | Leave a comment

JBrowse 1.10.11 maintenance release

JBrowse 1.10.11 has been released, with many bug fixes and better support for spliced alignments in SNPCoverage tracks.

(Download disabled.  Please download the 1.10.12 release or later instead.)

Minor improvements

  • Made the sequence track’s “zoom in to see sequence” placeholder
    take up less vertical space. Thanks to Scott Cain for pointing out
    that making it be the same height as it will eventually be when
    zoomed in to base level is silly.

  • By default highlighting features after searching for them by name
    is now turned off. Set the highlightSearchedRegions top-level
    conf variable to true to turn this back on. Turns out, most
    people seem not to like this behavior. Thanks to Gregg Helt and
    Cris Lawrence for pointing this out.

  • SNPCoverage tracks now correctly display “skipped” regions in
    alignments, such as those produced by TopHat. Thanks to Josh
    Orvis, Gustavo Cerquiera, and others for reminders that this was
    still an issue.

  • SNPCoverage tracks now provide per-strand counts of “reference”
    reads at each position, like they already were providing for
    reads with mismatches.

  • SNPCoverage tracks now accept a mismatchScale configuration
    variable that sets the viewing scale (i.e. zoom level, pixels per
    bp) above which base-level mismatches will be drawn. Defaults to
    1/10. Making this value larger can speed up SNPCoverage tracks for
    high-coverage data at the cost of needing to zoom in further to see
    mismatches.

  • setup.sh now uses curl for downloading things instead of wget,
    since curl is more widely available. Thanks to Keiran Raine for
    suggesting and implementing this (issue #393).

Bug fixes

  • Fixed a bug in which generate-names.pl would sometimes report the
    incorrect number of hashing bits in verbose output, and would
    sometimes use the number of hashing bits for an existing index even
    if that index was being regenerated. Thanks to Richard Hayes for
    pointing out the incorrect log output.

  • Fix generate-names.pl crashing on some older versions of Perl with
    an error like Bareword "POSIX::O_RDONLY" not allowed while "strict
    subs" in use
    . Thanks to Chris Childers for pointing this out.

  • Fix setup.sh failing on some older versions of Perl. It now runs
    generate-names.pl with the --safeMode flag.

  • Fixed a bug where the value display in SNPCoverage tracks would
    sometimes report “NaN%” for the reference when no reads cover a
    region.

  • Fixed a bug in which activating rubberband zooming using the SHIFT
    key while in highlighting mode would cause all the tracks to be
    dragged when attempting to highlight a region afterward. Thanks to
    Erik Derohanian for pointing out and fixing this (issue #387).

  • Fixed the location of the dojo/nls directory in release zipfiles.
    Was erroneously in src/nls, supposed to be src/dojo/nls. Thanks to
    Matt Bomhoff for pointing this out.

  • The in-memory GFF3 parser now copes with a missing newline at the
    end of a GFF3 file. Previously, the last line was ignored if it
    did not end with a newline character. Thanks to Colin Davenport
    for pointing this out (issue #394).

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