esvee v1.0-rc.1

Initial release, see READ-ME for full details

cobalt v2.0-rc.1

Technical

• handle missing ratio results from empty BAM
• ensure target regions file is sorted

chord v2.1-rc.1

Technical

• code refactor

bam-tools v1.3 release candidate 1

Functional:

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

Bugs:

• fixed tracking of consensus reads for coverage, counts and fragment lengths

Technical

• write partition statistics
• removing writing of old-style metrics file

amber v4.1 release candidate 2

No changes for WGS

Bugs:

• fixed restriction to panel regions in targeted mode

cuppa v2.3.0

Technical

• introduce Java entry point for prep + prediction
• compatible with Esvee

Bugs

• fix misalignment of cancer type in visualisation

fastq-tools v1.0.0-beta.1

Initial release of biomodal fastq collapse component.

To run this component use:

java -cp fastq-tools-v1.0.0-beta.1.jar com.hartwig.hmftools.fastqtools.biomodalcollapse.BiomodalCollapse \
  -threads $NUMBER_OF_THREADS \
  -fastq1 $PATH_TO_R1_FASTQ \
  -fastq2 $PATH_TO_R2_FASTQ \
  -out_fastq $COLLAPSED_FASTQ_OUTPUT_PATH

Note that you can restrict the tool to only process the first $N fragments by adding the argument -max_fastq_pairs_read $N to the above.

compar v1.3.0-beta.3

Description of release compar v1.3.0-beta.3

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.3

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