cuppa v2.2.1-beta.4

Description of release cuppa v2.2.1-beta.4

Full Changelog: cuppa-v2.2.1-beta.2...cuppa-v2.2.1-beta.4

cuppa v2.2.1-beta.3

Description of release cuppa v2.2.1-beta.3

Full Changelog: cuppa-v2.2.1-beta.2...cuppa-v2.2.1-beta.3

cuppa v2.2.1-beta.2

Description of release cuppa v2.2.1-beta.2

Full Changelog: cuppa-v2.2.1-beta.1...cuppa-v2.2.1-beta.2

teal v1.3.1

Small functional changes:

• Always use lenient BAM validation
• Change the pipeline mode calling to allow separating bam processing and telomere calculation stages.

virus-interpreter v1.5.0

Changes:

• Add blacklist option in order to blacklist HIV

orange v3.7.0

Changes:

• Add unreported reason to fusions in ORANGE
• Add etiology information to signatures and sort by allocation
• Add percentage of unsupported segments to Quality control page
• Show all viable fusions in ORANGE in samples where we detect no HIGH drivers
• Ensure HIV is never reported in ORANGE report or included in ORANGE json

esvee v1.0 beta

Beta 3 config & command changes:

Prep:

• class path: com.hartwig.hmftools.esvee.prep.PrepApplication
• bam_files -> bam_file

Assembly:

• class path: com.hartwig.hmftools.esvee.assembly.AssemblyApplication
• junction_files -> junction_file

Ref Depth Annotation:

• samples -> sample
• bam_files -> bam_file

Beta 4:

• LINE related improvements
• filters on discordant-only groups in prep and assembly

cuppa v2.2.1

Technical:

• Fixed out of memory error when running CuppaDataPrep on thousands of samples
• Removed matplotlib, plotnine, and mizani dependency
• Removed all code related to the old features format
• Other minor code clean ups

Functional:

• Added methods to read DataItem and DataItemMatrix from a TSV file

teal v1.3.0

Functional: ignore consensus reads created by redux

peach v2.0.0

Functional:

• Significantly change formats of input and output files.
• Handle overlapping genes correctly.
• Allow overlapping variants with different ref bases (deletions and insertions at the same location, overlapping SNVs and MNVs, etc.).
• Remove requirement to include both V37 and V38 coordinates in the resource files when calling on a V37 reference genome.

Technical:

• Converted from Python to Java.