Releases: mikessh/migec
Releases · mikessh/migec
1.2.9
Log update
1.2.8 2prev
JDK9 compatibility
- Now should work with Java 9
- Other minor fixes
N.B Please ignore
An illegal reflective access operation has occurredwarnings occurring when running with Java 9, they have no effect on software performance/output whatsoever
Hotfix for 1.2.5
Fixed classNotFound exception in Checkout.
As of now:
- A more-or-less realistic example data and shell script for migec pipeline is stored in
test/folder - Continuous integration will actually run the whole pipeline (including the BLAST'ing part): https://travis-ci.org/mikessh/migec
Minor fixes
Minor fixes for Checkout and Histogram
Homebrew compatibility fix
1.2.4a Version update
Shell script to invoke CLI + bug fix
The purpose of this release is to store binaries so that MIGEC can be installed with Homebrew package manager
- Add a shell script that simplifies invocation of MIGEC routines
- Fixed a bug with searching for reverse complemented D-segments.
Multi-chain mapping & database update
What's new
- Corrected V-(D)-J mapping in case several chains are specified
- Don't report chimeric alignments unless corresponding option is set
- No Diversity segment mapping is done for chains that don't have any
- Add missing Bos Taurus Variable segments database compiled, annotated and kindly provided by Deepali Vasoya, University of Edinburgh
New assembly feature and fixes
Features added
- Writing FASTQ with unmapped CDR3 with
--unmapped-fastq-filein CdrBlast - Some TRBV pseudogenes for mouse
- Option to use only the first read in Assemble and Histogram (
--only-first-read), useful for non-oriented reads when reverse read quality is very poor
Fixes
- Some CLI fixes, changed exit error codes
- Fix bug with incorrect calculation of min read size in Assemble
Multi-chain analysis and fixes
- Multiple chains can be specified for CdrBlast analysis, e.g.
-R TRA,TRB - Fix parsing of UMI headers with N characters
- Added missing TRD segments