PHAT 0.4.1

Downloads for This Release

• Windows Installer
• Ubuntu Linux Debian Package
• Windows Portable
• Linux Portable

  Experimental

• Red Hat Package Manager

Documentation for This Release

• Documentation

Browse Source Code for This Release

• Source for PHAT@0.4.1
• Source for PHAT

Changelog

• Split reference indexing into two options. Index for alignment, index for visualization
• Allow importing of BAM files produced externally
• Allow linking imported BAM files to inputted reference sequences for visualization
• #593
• Update checking will now abort if it takes too long to connect to github.com
• Startup performance improvements
• More aggressively save project manifest. Reduces chance of data loss in the event of operations crashing
• Fixed desync in alignment progress and QC report generation in new windows
• Allow importing of SAM files produced externally
• Allow linking imported SAM files to inputted reference sequences for visualizations
• Prototype process manager available by pressing Ctrl+1 in any window
• Startup and RAM improvements
• Added indentation and formatting to all operation logs, making them more readable
• Disable interactivity for large figures( >= 50 contigs or 1,000,000 BP)
• Disable rendering contig names for large figures
• Feed non interactive figures through the same SVG compilation pipeline as data tracks
• Added “Figure Options” dropdown for access to the same editing options available through interacting with the figure
• Interactivity and global contig name display toggles available through “Figure Options”
• Fixed installer GIF for Windows #628
  View full diff

250 Commits Since Last Release (0.1.5) (most recent last)

Chris Gibb: render table
Chris Gibb: barebones view
Chris Gibb: add linkrefview onmount
Chris Gibb: stop mounting all child views onmount
Chris Gibb: added props and data flow
Chris Gibb: allow view switching and render empty table
Chris Gibb: handler for go back button
Chris Gibb: proto linkability checks
Chris Gibb: added header and table rendering
Chris Gibb: init prop in ctor
Chris Gibb: removed logging
Chris Gibb: render start of incompatible table
Chris Gibb: throw if contigs is not valid
Chris Gibb: immediately reject unindexed refs
Chris Gibb: render incompatible table
Chris Gibb: show longreason on click
Chris Gibb: renamed and refactored method
Chris Gibb: method skeleton
Chris Gibb: removed var
Chris Gibb: proto find missing conigs method
Chris Gibb: report both statuses at once
Chris Gibb: skip last contig from samtools
Chris Gibb: Added docs
Chris Gibb: typed return type
Chris Gibb: proto linkrefseq operation harness
Chris Gibb: proto link process
Chris Gibb: added props
Chris Gibb: handler for link operation
Chris Gibb: fixed typo
Chris Gibb: move dir creation into function
Chris Gibb: run operation onclick
Chris Gibb: removed mkdir
Chris Gibb: moved mkdir into method
Chris Gibb: Fixed refs
Chris Gibb: fixed columns being pushed to the right
Chris Gibb: Fixed ref check
Chris Gibb: fixed check for unlinked alignment
Chris Gibb: render different props for external alignments
Chris Gibb: register new operations
Chris Gibb: module for imported bam from l6r1 hpv16 aligment
Chris Gibb: test for importing bam from l6r1 hpv16 alignment
Chris Gibb: removed logging
Chris Gibb: test link status
Chris Gibb: added noImplicitThis
Chris Gibb: test bam linking
Chris Gibb: Merge branch ‘master’ into importAlignments
Chris Gibb: Merge pull request #633 from chgibb/importAlignments External BAM Importing 593
Chris Gibb: Merge branch ‘beta-staging’ into master
Chris Gibb: Merge pull request #634 from chgibb/master External BAM Importing 593
Chris Gibb: Merge branch ‘beta’ into beta-staging
Chris Gibb: fixed typo
Chris Gibb: changed optimization order
Chris Gibb: Merge branch ‘importAlignments’ of https://github.com/chgibb/phat into importAlignments
Chris Gibb: Merge branch ‘importAlignments’ of https://github.com/chgibb/phat into importAlignments # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with ‘#’ will be ignored, and an empty message aborts # the commit.
Chris Gibb: Merge branch ‘master’ into importAlignments
Chris Gibb: Merge pull request #635 from chgibb/beta-staging External BAM Importing 593
Chris Gibb: Bumped to 0.2.0-beta.1
Chris Gibb: Merge pull request #636 from chgibb/importAlignments Startup Performance Improvements
Chris Gibb: save manifest after successful operations
Chris Gibb: get operations on startup
Chris Gibb: get operations on startup
Chris Gibb: get and sub to operations
Chris Gibb: fixed prop description
Chris Gibb: added loading text to all views
Chris Gibb: fixed progress updates
Chris Gibb: fixed broadcastin updates
Chris Gibb: display progress for relevant operations
Chris Gibb: fixed view transition when link is complete
Chris Gibb: fixed test for 0.00% alignment
Chris Gibb: tests for hpv18 bam importing
Chris Gibb: fixed test
Chris Gibb: added test for hpv18 bam linking
Chris Gibb: Merge branch ‘master’ into importAlignments
Chris Gibb: Merge pull request #639 from chgibb/importAlignments Loading Text for BAM Importing and Ref Indexing
Chris Gibb: Merge branch ‘beta-staging’ into master
Chris Gibb: Merge pull request #640 from chgibb/master Loading Text for BAM Importing and Ref Indexing
Chris Gibb: Merge branch ‘beta’ into beta-staging
Chris Gibb: added pid prop
Chris Gibb: Merge pull request #641 from chgibb/beta-staging Loading Text for BAM Importing and Ref Indexing
Chris Gibb: Bumped to 0.2.0-beta.2
Chris Gibb: stop logging on handled failure
Chris Gibb: expand filter to include sams
Chris Gibb: added null check
Chris Gibb: allow sam inputting
Chris Gibb: added tests for sam importing
Chris Gibb: update alignment sizes after operations
Chris Gibb: Merge branch ‘master’ into importAlignments
Chris Gibb: Merge pull request #642 from chgibb/importAlignments SAM Importing
Chris Gibb: Merge pull request #643 from chgibb/master Update Feature Branch
Chris Gibb: Merge branch ‘beta-staging’ into master
Chris Gibb: fleshed out pid registration
Chris Gibb: added prop
Chris Gibb: added fork detection method
Chris Gibb: pass pids through to main
Chris Gibb: register pids
Chris Gibb: register forks pids
Chris Gibb: bumped electron version
Chris Gibb: changed protocol type
Chris Gibb: method to retrieve pids for all open windows
Chris Gibb: ipc endpoint to retrieve all application pids
Chris Gibb: Merge pull request #644 from chgibb/master SAM Importing
Chris Gibb: Merge branch ‘beta’ into beta-staging
Chris Gibb: window creator for procmgr
Chris Gibb: added process manager to app menu
Chris Gibb: created barebones html + css for procmgr
Chris Gibb: bootstrapper for procmgr
Chris Gibb: bare renderer for procmgr
Chris Gibb: barebones renderer
Chris Gibb: skeleton view
Chris Gibb: fixed replychannel
Chris Gibb: include the main process’ pid
Chris Gibb: bare process view
Chris Gibb: added procview
Chris Gibb: added package
Chris Gibb: proto pidinfo module
Chris Gibb: split up module
Chris Gibb: added method for returning all open windows
Chris Gibb: broadcast as much information as possible
Chris Gibb: added package
Chris Gibb: added props
Chris Gibb: added method for resource usage
Chris Gibb: handle processes which have already closed
Chris Gibb: added style imports
Chris Gibb: added passhrough
Chris Gibb: proto table rendering
Chris Gibb: fixed sort
Chris Gibb: make default size smaller
Chris Gibb: truncate digits on output
Chris Gibb: Merge pull request #645 from chgibb/beta-staging SAM Importing
Chris Gibb: Bumped to 0.2.0-beta.3
Chris Gibb: changed to import
Chris Gibb: added package
Chris Gibb: support cli arg for production build
Chris Gibb: renamed switch to opt
Chris Gibb: added compiler config for optimized js compile pipeline
Chris Gibb: apply rollup before broserify for opt builds
Chris Gibb: run opt build before opt passes
Chris Gibb: fixed rollup incompatibilities
Chris Gibb: added switch
Chris Gibb: Merge branch ‘master’ into procMgr
Chris Gibb: Merge pull request #646 from chgibb/procMgr Process Manager
Chris Gibb: Merge branch ‘beta-staging’ into master
Chris Gibb: renamed symbol
Chris Gibb: Merge pull request #647 from chgibb/master Process Manager
Chris Gibb: Merge branch ‘beta’ into beta-staging
Chris Gibb: reverted rename
Chris Gibb: added prop
Chris Gibb: differentiate between interactive/non interactive figures
Chris Gibb: renamed var
Chris Gibb: clear basefigure svg string on reload
Chris Gibb: removed old code
Chris Gibb: cache logic for basefigure svg
Chris Gibb: refresh caches on displaying non interactive figures
Chris Gibb: broke fetching track svgs into function
Chris Gibb: broke div removal into function
Chris Gibb: export var
Chris Gibb: reconstruct div on rerender
Chris Gibb: allow reseting of base figure
Chris Gibb: handle response from base figure compilation
Chris Gibb: differentiate between interactive and non ineractive contigs when rendering
Chris Gibb: disable figure name hovering when noninteractive
Chris Gibb: don’t render contig names for large figures
Chris Gibb: noop if figure is non interactive
Chris Gibb: recompile base figure in function
Chris Gibb: renamed function
Chris Gibb: added figure options dropdown
Chris Gibb: turn off interactivity for figures with large number of bp
Chris Gibb: remove markerclass only when noninteractive
Chris Gibb: added logging
Chris Gibb: removed logging and fixed exit
Chris Gibb: Bumped to 0.3.0-beta.1
Chris Gibb: Merge branch ‘beta’ into beta-staging
Chris Gibb: Merge pull request #649 from chgibb/beta-staging Process Manager
Chris Gibb: Bumped to 0.3.0-beta.1
Chris Gibb: Bumped to 0.3.0-beta.1
Chris Gibb: method to gracefully exit forks
Chris Gibb: move to using exitFork
Chris Gibb: abstracted out forking
Chris Gibb: start using makefork for selected operations
Chris Gibb: moved all to makefork
Chris Gibb: revert commented out method
Chris Gibb: use exitFork for all operations
Chris Gibb: use exitFork during fork failure
Chris Gibb: add formatting to logs
Chris Gibb: added UI toggles for interactivity and showing contig names
Chris Gibb: added method to delete svgs for base figures
Chris Gibb: delete svg in method
Chris Gibb: made function synchronous
Chris Gibb: removed trailing comma in import
Chris Gibb: fixed radius update for non interactive figures
Chris Gibb: trigger recompile for figure on track interval change
Chris Gibb: recompile on interval display change
unknown: Added my name.
Zack: Added my name to Team Members list
Chris Gibb: Merge pull request #650 from chgibb/readmeNick Added my name.
Chris Gibb: Merge branch ‘master’ into readmeZack
Chris Gibb: Merge pull request #651 from chgibb/readmeZack Added my name to Team Members list
Chris Gibb: removed old code
Chris Gibb: log return codes for forks
Chris Gibb: exit after callback
Chris Gibb: added dropdown option for editing figure name
Chris Gibb: reset caches for non interactive figures
Chris Gibb: refactored saving changes and fixed update for non interactive figures
Chris Gibb: added dropdown option to edit contigs
Chris Gibb: open edit contigs modal onclick
Chris Gibb: barebones edit contigs modal
Chris Gibb: render reference contigs with hover
Chris Gibb: click to edit custom contigs
Chris Gibb: click to edit reference contigs
Chris Gibb: fixed figure update for non interactive figures after saving changes to a contig
Chris Gibb: fixed track loading text
Chris Gibb: fixed noninteractive resizing and interval updates
Chris Gibb: Merge branch ‘master’ into 648
Chris Gibb: commented modules
Chris Gibb: Merge branch ‘648’ of https://github.com/chgibb/phat into 648
Chris Gibb: added comments
Chris Gibb: Merge pull request #652 from chgibb/648 Non-Interactive Figures
Chris Gibb: Merge branch ‘beta-staging’ into master
Chris Gibb: Merge pull request #653 from chgibb/master Non-Interactive Figures
Chris Gibb: Merge branch ‘beta’ into beta-staging
Chris Gibb: Merge pull request #654 from chgibb/beta-staging Non-Interactive Figures
Chris Gibb: Bumped to 0.4.0-beta.1
RobJackson28: Added pressed alignButton
Chris Gibb: Merge pull request #655 from chgibb/RobJackson28-patch-11 Added pressed alignButton
Chris Gibb: removed menu item for procmgr
Chris Gibb: moved procmgr invoke to pressing “1” key with prompt about being experimental
Chris Gibb: added comment
Chris Gibb: Merge pull request #656 from chgibb/638 638
Zack: changed param passing
Zack: Merge branch ‘readmeZack’ of http://github.com/chgibb/phat into readmeZack
chgibb: deleted old installer gif
chgibb: renamed new installer gif
Chris Gibb: Merge branch ‘master’ into readmeZack
Chris Gibb: Merge pull request #660 from chgibb/628 628
Chris Gibb: Merge branch ‘master’ into readmeZack
Chris Gibb: changed from “1” to Ctrl+”1”
Chris Gibb: Merge branch ‘master’ into 628
Chris Gibb: Merge pull request #659 from chgibb/readmeZack Fixed Error in GCC 6/7
Chris Gibb: Merge branch ‘master’ into 628
Chris Gibb: Merge pull request #661 from chgibb/628 changed from “1” to Ctrl+”1”
Chris Gibb: Merge branch ‘beta-staging’ into master
Chris Gibb: Merge pull request #662 from chgibb/master 638, 628
Chris Gibb: Merge branch ‘beta’ into beta-staging
Chris Gibb: Merge pull request #663 from chgibb/beta-staging 638, 628
Chris Gibb: Bumped to 0.4.1-beta.1
Chris Gibb: Merge branch ‘stable-staging’ into beta
Chris Gibb: Merge pull request #665 from chgibb/beta Promote 0.4.1-beta.1 to 0.4.1
Chris Gibb: Merge branch ‘stable’ into stable-staging
Chris Gibb: Merge pull request #668 from chgibb/stable-staging Promote 0.4.1-beta.1 to 0.4.1
Chris Gibb: Bumped to 0.4.1