View on GitHub

PHATDocs

Documentation for https://github.com/chgibb/phat

PHAT 0.10.1

Downloads for This Release

Documentation for This Release

Browse Source Code for This Release

Changelog

66 Commits Since Last Release (0.9.2) (most recent last)

Chris Gibb: Update README.md
Chris Gibb: Merge pull request #821 from chgibb/beta Backport Merges and Version
Chris Gibb: Update README.md
Chris Gibb: Merge pull request #824 from chgibb/stable Backport Merges and Version
Chris Gibb: bumped version
Chris Gibb: renamed operation
Chris Gibb: override vscode file watcher settings
Chris Gibb: index fasta prior to alignment
Chris Gibb: removed old smoke test step and fixed wait for nonexistent operation
Chris Gibb: remove redundant asyncs
Chris Gibb: remove ref indexing from gui
Chris Gibb: initial hisat2 download and bundling
Chris Gibb: ignore compiled sources in editor
Chris Gibb: normalize naming for alignments and start adding hisat2 specific plumbing code
Chris Gibb: normalize more path and file names. Hisat2 index and build plumbing. Start hisat2 index tests
Chris Gibb: include failed index file in error message
Chris Gibb: hisat2 indexing operation plumbing
Chris Gibb: don’t require writing of rev.x.ht2 indices
Chris Gibb: expand file exclusion lists
Chris Gibb: hisat2 hpv18 index and hpv16 alignment tests
Chris Gibb: L6R1 hpv16 and hpv18 hisat2 tests
Chris Gibb: fixed typing
Chris Gibb: fixed glob to ignore compiler artifacts
Chris Gibb: fixed hisat2 path quoting
Chris Gibb: refactored promise chains and tightened test success criteria for alignments
Chris Gibb: show aligner used in output and genome builder
Chris Gibb: expanded modal to fit wider tables. Fixed modal transition error
chgibb: initial hisat2 windows bundling
chgibb: ignore app directoy in vscode
chgibb: explicitly reject and resolve
chgibb: changed quote use and use of perl
chgibb: reject on error
chgibb: explicitly return
chgibb: download linux version on windows for invoke script. Clean artifacts after copying out needed files
chgibb: download hisat2 archives on start
Chris Gibb: converted tab to spaces
Chris Gibb: removed old invoke method
Chris Gibb: Merge pull request #825 from chgibb/hisat2 Hisat2
Chris Gibb: Merge pull request #827 from chgibb/master 0.10.0-beta.1
Chris Gibb: Merge pull request #828 from chgibb/beta-staging 0.10.0-beta.1
Chris Gibb: Bumped to 0.10.0-beta.1
Chris Gibb: Update README.md
Chris Gibb: Merge pull request #829 from chgibb/beta Promote 0.10.0-beta.1 to Stable
Chris Gibb: stop calling disconnect on exit from fork
Chris Gibb: Update citation to point to Bioinformatics
Chris Gibb: updated readme citation
Chris Gibb: make processes opt out of disconnecting IPC channel by default. Opt out InputBamFileProcess
Chris Gibb: Merge pull request #831 from chgibb/citation Update Citation Links
Chris Gibb: function to retrieve full operation log content
Chris Gibb: print content of operation logs on test failures
Chris Gibb: fix file eol
chgibb: fixed spacing and use ws regex
chgibb: fix escape in ws regex
chgibb: added unit test for bowtie2 report parsing
chgibb: refactor report parsing step and add another test case
chgibb: delay resolution
Chris Gibb: Removed pre-print notice
Chris Gibb: Merge branch ‘master’ into ci
Chris Gibb: Merge pull request #832 from chgibb/ci CI Fixes
Chris Gibb: Merge pull request #833 from chgibb/master Update Citation and CI Fixes
Chris Gibb: Merge branch ‘beta’ into beta-staging
Chris Gibb: Merge pull request #834 from chgibb/beta-staging Update Citation and CI Fixes
Chris Gibb: Bumped to 0.10.1-beta.1
Chris Gibb: Merge pull request #835 from chgibb/beta Promote 0.10.1-beta.1 to Stable
Chris Gibb: Merge pull request #837 from chgibb/stable-staging Promote 0.10.1-beta.1 to Stable
Chris Gibb: Bumped to 0.10.1