PHAT 0.2.0-beta.1

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• 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@0.2.0-beta.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

  122 Commits Since Last Release (0.1.5-beta.1) (most recent last)

  Chris Gibb: Merge pull request #605 from chgibb/stable-staging Promote 0.1.1-beta.7 to 0.1.1
  Chris Gibb: Bumped to 0.1.1
  Chris Gibb: changed condition for link generation
  Chris Gibb: renamed file
  Chris Gibb: Merge pull request #622 from chgibb/beta Promote 0.1.4-beta.1 to 0.1.4
  Chris Gibb: Merge branch ‘stable’ into stable-staging
  Chris Gibb: Merge pull request #624 from chgibb/master Update Feature Branch
  Chris Gibb: Added newline
  Chris Gibb: Added bare align view
  Chris Gibb: Added empty table and tab switching
  Chris Gibb: fleshed out table
  Chris Gibb: subscribe to aligns
  Chris Gibb: added prop
  Chris Gibb: passthrough aligns on update
  Chris Gibb: differentiate between indexing for aligning vs indexing for viz
  Chris Gibb: promise wrapper for contig loader
  Chris Gibb: refactored to use await
  Chris Gibb: fixed image
  Chris Gibb: renamed file
  Chris Gibb: refactored export
  Chris Gibb: removed files
  Chris Gibb: Updated gitignore
  Chris Gibb: Fixed startup flag warnings
  Chris Gibb: Renamed operation
  Chris Gibb: renamed file
  Chris Gibb: Fixed import paths
  Chris Gibb: Split indexfastaforalignment into two operations
  Chris Gibb: don’t try to view alignments with unindexed refs
  Chris Gibb: bail out if connection can’t be established
  Chris Gibb: start viz indexing onclick
  Chris Gibb: endpoints for viz indexing
  Chris Gibb: check original fasta for index status
  Chris Gibb: added props
  Chris Gibb: get contigs and set prop on success
  Chris Gibb: set prop on success
  Chris Gibb: set props on success
  Chris Gibb: added props
  Chris Gibb: set flags on success
  Chris Gibb: fixed display checls
  Chris Gibb: added test for hpv16 visualization index
  Chris Gibb: added test for hpv18 visualization indexing
  Chris Gibb: don’t reparse contigs
  Chris Gibb: rewrote contig loader
  Chris Gibb: commented figure methods. Refactored SNP rendering
  Chris Gibb: removed old code
  Chris Gibb: Fixed indexing variables
  Chris Gibb: barebones bam dialog
  Chris Gibb: added prop
  Chris Gibb: Merge branch ‘stable-staging’ into beta
  Chris Gibb: barebones input bam process
  Chris Gibb: barebones input bam operation
  Chris Gibb: barebones operation integration
  Chris Gibb: start operation for each selected bam
  Chris Gibb: delete output dir on failure
  Chris Gibb: copy and sort bam
  Chris Gibb: create if undefined
  Chris Gibb: set prop on init
  RobJackson28: Updated installer GIF (square)
  Chris Gibb: barebones samtools flagstat harness
  Chris Gibb: proto flagstat harness
  Chris Gibb: render row for external alignments
  Chris Gibb: extract reads from flagstat report
  Chris Gibb: selectively render bowtie2/flagstat values
  Chris Gibb: Merge pull request #631 from chgibb/RobJackson28-patch-10 Updated installer GIF (square)
  Chris Gibb: prevent viewing alignment with no ref
  Chris Gibb: prevent viewing of unlinked alignment
  Chris Gibb: index and get idxstats
  Chris Gibb: added checks for unlinked, imported bams
  Chris Gibb: set alias as filename
  Chris Gibb: fixed subscription
  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: Merge pull request #635 from chgibb/beta-staging External BAM Importing 593
  Chris Gibb: Bumped to 0.2.0-beta.1