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v6.3.4

  • Bedtools 2.28.0 binary caused stack collision.
  • Fix R package gam to 1.16.1 due to change in behaviour of 1.20 (5th July 2020).

v6.3.3

  • Singularity specific execution issue corrected

v6.3.2

  • Fix edgecase on RG line handling (#99)
  • Ensure attempt to run on completion give exit==0 (#98)

v6.3.1

  • Handle undefined value edge case #95.
    • Thanks to @udvzol for reproducible test data.
  • Updated travis build (#89)
  • Fixed up dockerfile to reduce build time when testing.

v6.3.0

  • Adds stand alone (supported) docker container

v6.2.1

  • Resolves #85 - command line help
  • Resolves #86 - blatSrc code moved

v6.2.1

  • Fixes #80 - allow RGID == 0
  • Resolves #84 - use helper threads where possible

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

  • Change tabix->query to tabix->query_full

v6.1.1

  • Reduce I/O for small cpu overhead in coverage step
  • Fix assembly step to cope with bam.csi and cram.crai
  • R lib issues and disable diagnostic plots.

v6.1.0

  • Add travis-ci
  • Fix #46
  • Correct removal of overlapping reads (small number of bad reads passed to grouping phase).
    • See 508112837271853152ca48d1ecad5a443fadefbb
  • Reworked readme and reference dockstore/docker/singularity

v6.0.5

  • Fix ssearch36 queries attempting to get sequence beyond start of chromosome/contig.

v6.0.4

  • Modify Rsupport/libInstall.R to cope with use of R <3.4 for standard builds
    • If you use newer build of R install VGAM as other bioconductor libs
  • Change install method in libInstall.R to physically exit with error state if library fails to build
  • Add a fixed seed (42) to metropolis_hastings_inversions.R to ensure reproducible results

v6.0.2

  • 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

v6.0.0

  • Modified mormal panel is now handled in more efficient way - makes BRASS GROUP step extremly faster

v5.4.1

  • Fix bug in implementation of cytoband option.

v5.4.0

  • pcf function in copynumber package is now species agnostic
  • removed NA rows before applying gam function

v5.3.4

Merge fix for clang compilation, thanks to @jmarshall

v5.3.2

Fixed #51

v5.3.1

Fixed #42, #43, #50

v5.3.0

  • Removed dependency on bedGraphToBigWig and use bg2bw from cgpBigWig (already dep. for PCAP-core).