Speedups

• Speedups in callback methods
• Addition of IntervalTree use instead of tabix

1.8.8 - unmatched normal panel processing

Depending on tools used to manipulate the VCF form of the unmatched normal panel there are multiple possible formats for a sample genotype where no data was collected.

This hotfix includes the following modifications

1. Legacy and new versions of flagging code will consider 0:.:.:.:., -, . as "no data for sample"
2. convertVCFUnmatchedToBed.pl updated as in (1).

If you are using pre-generated normal panels from our FTP site this doesn't affect you and there is no need for urgent upgrade.

Hotfix - 1.8.5

• Added TARGETED to GRCh38 human config ini

add 3 soft flags to all config

added 3 soft flags (CLPM, ASMD and ASRD) to all species builds and design_types (except RNAseq)

1.8.0 - Overlapping read support

1.8.0

• Overlapping reads now handled
• Updates to licenese headers and contact information
• Support for csi and crai indexes
• README cleanup
• Ability to exclude contigs from analysis

Release candidate - Overlapping reads

1.8.0-rc1

License years update

Hotfix - 1.7.2 - Updating reference data in ini files

• Updating species config files to ensure they always point to gz files

Hotfix - 1.6.10 - Now fails if no flaglist present

Convert warning to error where no flags were included in list

Hotfix - 1.7.1 - Warning should have been fatal

• Convert warning to error where no flags were included in list
• Added species and build specific config files

Feature - 1.7.0 - added Travis CI testing

• Added travis testing