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1.19.0

  • Update to caveman 1.15.4
  • Update Dockerfile to include copying generateCavemanUMNormVCF into the image, and tweak CI to understand that
  • Update Dockerfile to use setup.sh install method from caveman repo and ensure linasm.so is on LD PATH

1.18.3

  • Update CaVEMan core to 1.15.3
  • Removes requirement for CWD as this can break nf

1.18.2

  • Update CaVEMAn core to 1.15.2
  • Minor bugfix in VCF output. Genotypes now output as unphased rather than phased.

1.18.1

  • Updated to cgpCaVEManPostProcessing 1.12.0

1.17.5

  • Upgrade to cgpCaVEMAnPostProcessing 1.11.0
    • Now able to accept yaml format flagging ini file

1.17.4

  • Updated cgpCaVEManPostProcessing to 1.9.3

1.17.3

  • Updated cgpCaVEManPostProcessing to 1.9.2

1.17.2

  • Updated CaVEMan core to 1.15.1

1.17.1

  • Updated Dockerfile to use PCAP-core 5.4.0 - samtools/htslib 1.11

1.17.0

  • Updated Dockerfile to use PCAP-core 5.2.2
  • Updated setup.sh script to remove redundant logic
  • Updated CaVEMan core to 1.15.0

1.16.0

  • Pulls in cgpCaVEManPostProcessing 1.9.0
    • Edgecase fix for overlapping reads - cause +1 variant at WGS scale
    • Major performance improvement (in post processing)

1.15.3

  • Build around CaVEMan core 1.14.1

1.15.2

  • Upgrade to cgpCavEMAnPostProcessing 1.8.9

1.15.1

  • Force all executed command output to logs/*.{out,err}, other method seems to behave oddly under singularity

1.15.0

  • Build around CaVEMan core 1.14.0 - uses linasm and read_position calculation speedups
  • Add linasm installation to Docker build scripts
  • Change base Docker build to quay.io/wtsicgp/pcap-core:4.4.0

1.14.1

1.14.0

  • Created Docker file to build a containder for the wrapper.
  • Added quay.io badge for the image to the README.

1.13.14

  • Adds -noclean option to allow resumption following -noflag execution.

1.13.13

1.13.12

  • Minor errors in CaVEMan 1.13.13 force update.

1.13.11

  • Add AMPLICON and TARGETED to accepted protocol list. Change RNA-seq, but also keep RNA.
  • protocol list
  • In line with Update of CaVEMan:
  • Build with CaVEMan 1.13.13

1.13.10

  • Fix command line parsing of short option names, np/NP and tp/TP only ever set uppercase versions.

1.13.9

1.13.8

  • Added libdb-dev and libgd-dev to travis.yml

1.13.7

1.13.6

  • Build with CaVEMan 1.13.10
  • See CaVEMan changes below

Behaviour change

-Where the proper pair filter flag is used, this code now checks that the paired-end orientation is also used.* -This will mean that mate-pair orientation (F/F or R/R) will be rejected* -If you wish to use mate-pair data, please use previous version*

  • Where a proper pair filter is used, now check for the correct paired-end orientation of F/R.
  • If this is not met the read is ignored.

1.13.5

1.13.4

1.13.3

1.13.1

1.13.0

  • Overlapping read support
  • Support for csi indexing of bam/cram files
  • Scatter gather implememnted for flagging
  • Updates to README, license dates and contact information
  • Uses CaVEMan core overlapping reads enabled 1.13.0

1.12.0

  • Update to use CaVEMan 1.12.0
  • Deal with CaVEMan 1.12.0 intermediate output now being gzipped