v6.3.4 - bedtools errors

Bedtools causing stack collision errors on subset of processing, updated to 2.29.2 appears to resolve.

Also had to fix R library gam to version 1.16.1 due to failures with very new 1.20 version.

v6.3.3 - singularity edgecase

Issue only occurs under Singularity execution of pulled docker container. Error along lines: binary file cannot be executed.

v6.3.2 - fix edge case due to field order in RG headers

• Fix issue caused by ID bring final element of RG header #99.
• Also fixes #98

v6.3.1 - fix edgecase

Fix undefined value when refining breakpoints.

Change has no impact on large scale internal testing result.

Docker image will be available via: docker pull quay.io/wtsicgp/brass:v6.3.1

(https://quay.io/repository/wtsicgp/brass)

v6.2.1 - hotfix

• Resolves #80
  • Fail when RG==0
• Resolves #84
  • use helpers when reading inputs

v6.2.0

• Fixed bug where subset of intervals does not have reads -issue#65
• Informative error when .bas file is absent - issue #71
• temp file were now kept after running filter step - issue #73
• Fixed issue #66
• Added script to process centro/telomere data - issue #70
• Fixed bug where intermediate file name matches with one of the sample

v6.1.2 - Hotfix tabix->query to query_full

v6.1.2

• Change tabix->query to tabix->query_full

fix instance of 'keys on reference'

Only an issue if installation fails on 6.0.5 due to later versions of perl promoting this to a fatal error.

v6.0.5 - Refseq out of range

Events close to start of contigs (<1kb) attempted to select from fasta file with negative values. This resolves this by setting min value of 1.

Errors like the following are the symptom:

Use of uninitialized value in uc at /.../bin/filter_with_microbes_and_remapping.pl line 216.

or

Use of uninitialized value in transliteration (tr///) at /.../bin/filter_with_microbes_and_remapping.pl line 529.

v6.0.2 - Prevent result instability

• Fixes instability in results due to unsorted keys used in outputs.
  • Perls 5.18+ give variability on duplicate runs as hash keys have enforced randomisation. Found all relevant instances, outputs are now stable between runs and perl versions.
• Shortened paths in *.intermediates.tar.gz