CHANGES

3.7.0

Update base image to Ubuntu 20.04

3.6.1

Missing command line arg description in addVagrentContext.pl

3.6.0

Adds addVagrentContext.pl to replace unsupported internal code.
Cleans up some of the build processes

3.5.2

Make errors emit non-zero exit codes #39
Cleanup input option #38

3.5.1

Handle chr not present in itree hash when running Admin_GeneRegionBedDumper.pl

3.5.0

Loads vagrent cache into IntervalTree to speed up processing by:
- reducing redundant/random disk access
- reducing repeated decompression of same data when events are local to each other

3.4.0

Add Dockerfile and supporting scripts
Switch travis-ci to build and test under docker

3.3.5

fixing pipefail issue for non-bash environments, splitting command into 2 separate executions.

3.3.4

Don't assume working directory is writable (fixes #33)

3.3.3

fixing issue in Admin_CacheFileBuilder.pl where it would fail without the optional fai file

3.3.2

Actually get the new htslib and samtools links correct in setup.sh
Move samtools install in setup.sh to happen before Bio::DB::HTS

3.3.1

samtools and htslib updated to 1.7
Bio::DB::HTS updated to 2.10, fixes error with GRCh38 contig names in Tabix.
Update tabix query to use query_full

3.3.0

Complete re-write of the reference generation code

3.2.2

Add bedtools2 to setup.sh
Added bedtools2 to README.md
Changes Bio::DB::HTS, samtools and HTSlib install methods.
Corrected condition indicating sort is required.
Fixes #23 Changed from vcf-sort to normal linux sort to ensure multiple indels with same start coord are sorted in a stable way.

3.2.0

Allows use of ensemblgenomes.org as a datasource
Handle genes without names, and give more useful error message
Ensure an error code is emmitted on failure

3.1.0

Adds travis testing
Cleans up install script and adds multi versioned paths to options

3.0.0

Removed use of legacy Tabix codebase and switches to samtools 1.2+
Switches to gihub version of vcftools and makes several patches unnecessary
Several bugfixes