v-chord v0.1_beta.1

Description of release v-chord v0.1_beta.1

Full Changelog: compar-v1.3.0-beta.2...v-chord-v0.1_beta.1

compar v1.3.0-beta.2

Description of release compar v1.3.0-beta.2

What's Changed

DEV-3784: Add liftover for somatic disruptions and germline variants and disruptions.
Make compatible with Cuppa v2.
DEV-4061: Add many fields and new categories: PEACH, VIRUS, TUMOR_FLAGSTAT, GERMLINE_FLAGSTAT, TUMOR_BAM_METRICS, GERMLINE_BAM_METRICS, SNP_GENOTYPE.
Removed support for old format germline SV file.
Adjusted disruption comparison to be less dependent on exact position.
DEV-4082: Create INVALID_ERROR output when error is thrown in comparison
DEV-4084: Fix problems in disruption comparison
Add categories: CDR3_SEQUENCE, CDR3_LOCUS_SUMMARY, TELOMERE_LENGTH

Full Changelog: compar-v1.2...compar-v1.3.0-beta.2

orange v3.7.1_beta

Description of release orange v3.7.1_beta

What's Changed

• ACTIN-292: Add Chromosomal Rearrangements by @cbruel in #612
• DEV-4083: Incorporate biallelic probability in Orange by @DFKoetsier in #615
• Fix crashing on samples containing no data (e.g. no template controls (NTC))

Full Changelog: cuppa-v2.3.0_beta...orange-v3.7.1_beta

chord v2.1.0 beta

Beta 0:

• Reimplemented mutSigExtractor R package in java

Beta 1:

• Replace CHORD R package with an R script and java wrapper
• Exclude variants where FILTER is '.' when selecting PASS variants

Beta 2:

• Fix ChordDataPrep not working on hg38 by storing chromosomes from VCF as String rather than HumanChromosome

cuppa v2.3 beta

Beta 0:

• Use latest SV factory

Beta 1:

• Fix misalignment of cancer type columns in visualization heatmap

cuppa v2.2.1-beta.19

Description of release cuppa v2.2.1-beta.19

Full Changelog: cuppa-v2.2.1-beta.9...cuppa-v2.2.1-beta.19

cuppa v2.2.1-beta.18

Description of release cuppa v2.2.1-beta.18

Full Changelog: cuppa-v2.2.1-beta.10...cuppa-v2.2.1-beta.18

virus-interpreter v3.7 beta

virus-interpreter-v3.7_beta

Version 3.7 beta

sage v4.0 beta

Sage beta 2:

• fixed read context cigar VCF tag, affects SageAppend deserialisation

Sage beta 3:

• Parse sage version in vcf using ModuleDescriptor.Version

redux v1.0 beta

Beta 2:

• set mate unmapped for consensus read with non-human contig read

Beta 3:

• protect against ref base look-ups past end of chromosome
• synchronise calls to process completed read groups for consensus, relevant when reprocessing supplementaries
• use 'redux' in TSV output files

Beta 4:

• use supp BAMs by default, disable with config 'no_supp_bam'
• consensus ref genome end of chromosome fix
• unmap secondaries and drop from BAM