Collapsed mode for track header

Now it's possible to view tracks in a "collapsed" mode. This mode hides a track header to provide more space for data (reduces each track height by 21px)

Collapsed mode:

In collapsed mode track headers are shown as floating semi-transparent bars in the top right corner of the track

Clicking a "hamburger" menu icon opens a track menu (shown on the track header in "non-collapsed" mode):

To enable/disable "collapsed" mode use "Settings -> General -> Tracks" menu:

More vertical space for data

The following changes provide even more vertical space for data:

• Global ruler height reduced by 36px
• Panels tabs' height reduced by 9px
• Variant table row height reduced by 13px

Open files without registration

Now it is possible to open files (BAM, VCF, GFF/GTF, BED) without registration.

"Open file" menu item added to the left toolbar providing two options (both of them require tbi index for the feature files and bai index for alignments being loaded):

• "From NGB Server":

• "From URL":

Build process and installation changes

• Build process is moved from build.sh to gradle, thus eliminating dependency on bash environment. See README for a list of commands
• install.sh script removed in favour of a standalone springboot jar

URL format changes

Several changes to NGB URL format (aimed to simplify embedding NGB):

• Specifying file names instead of IDs for a &tracks parameter
• Specifying all dataset tracks by using only p option of a &tracks parameter
• Filter datasets by genome (&filterByGenome=hg19)
• Display track headers in a collapsed mode by default (&collapsedTrackHeaders)
• Select first chromosome for a reference genome, in case a name is not known ({first-chromosome} should be set as a chromosome name)

Previously track ("b") and parent dataset ("b") had to be integer identifiers:

tracks=[{"b":7,"p":1}]

Now these options should preferably be specified as names (given at registration):

tracks=[{"b":"sv_sample_1.vcf","p":"SV_sample1"}]

For more details see Embedding guide

NGB Command Line Interface changes

• Several changes to NGB CLI (see NGB CLI Command Reference for details):
  • url command added to NGB CLI. It generates an URL that allows launching NGB with a set of opened files and at a specific genome position
  • Reference FASTA files now are registered without converting to internal "nib" format thus significantly decreasing the registration time
  • -ngc option added to reg_ref command, telling NGB not to calculate GC-content values for a reference track

NGB standalone desktop version preview

A preview version of a desktop version is added. This version runs locally on

• Windows
• MacOS
• Linux

Desktop version includes both NGB Java server and JS client packaged into a single platform-specific executable, using Electron framework

4 genomes are available out of the box to start using desktop version immediately:

• GRCh38
• GRCh37
• D.melanogaster
• Mus musculus

Sources are provided in a /desktop folder of the repository.

Details on building desktop version are provided in a desktop README

Other changes

• NGB supports Apple Safari now
• "Close all tracks" button added to the "Browser" panel:

• "Create session" button moved to the left toolbar: