v3.7.0 - Update base image to Ubuntu 20.04

Updated the base image to Ubuntu Focal (20.04)

v3.5.0 - Speedup

Considerable improvement to speed by loading cache file into in memory interval tree. Please review command line args for new parameters.

v3.3.5 - Issue with Admin_GeneRegionBedDumper.pl

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

v3.3.3 - Issue with Admin_CacheFileBuilder.pl

Inadvertently made the optional fai file compulsory, now fixed.

v3.3.2 - Correct setup.sh for new Bio::DB::HTS install

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

v3.3.1: * `samtools` and `htslib` updated to 1.7

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

v3.3.0 - Re-write of the reference generation code

This release contains a complete replacement for the cache file generation code.

• Should make it function over a wider variety of Ensembl versions/species
• Decision tree for choosing which transcripts to include has changed
• The cache file format has not been changed

If you regenerate an existing cache file with the new code base it will be compatible with older versions of VAGrENT but may not be identical. The set of transcripts included is quite likely to have changed.

v3.2.3 - Sorting of internal fields

Fixes to ensure content of info fields is stable between runs, not just the order of vcf records.

See #25

v3.2.2 - Stable sorting for events with same start

Primarily fixes various issues relating to sorting.

Specific issues addressed:

• #22
• #23

v3.2.1

Update htslib version to bring CGP stack in line