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.

orange v3.6.0

Changes:

• Cuppa predictions with NaN likelihood are filtered in the ORANGE conversion of CUPPA results

wisp v1.2 beta

Functional:

• added Amber LOH method
• refined various aspects of somatic variant purity calculations

cuppa v2.2.0

Functional:

• Added full multi-sample support (updated Python and R components)
• Adapted CuppaDataPrep to accept generic somatic variant tsv files

Technical:

• Remove deprecated code used in CUPPA v1

bam-tools v1.3 beta

Functional:

• count overlapping bases towards standard coverage
• allow reads partially overlapping a targeted region in target-only mode

Bugs:

• handle remove reads in any contig (ie not just standard human chromosomes)
• fix tracking on flag stats for consensus reads

sage v3.4.4

Technical:

• use minimum sequence dictionary in sync fragment consensus read building. Improves performance when ref genome has a high number of alt contigs