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Recent Releases of https://github.com/cancerit/cgpcavemanwrapper

https://github.com/cancerit/cgpcavemanwrapper - 1.19.0 - caveman 1.15.4 and generateCavemanUMNormVCF support

Includes generateCavemanUMNormVCF in image, and updates install process in dockerfile to provide depedencies for that tool

- Perl
Published by blex-max almost 2 years ago

https://github.com/cancerit/cgpcavemanwrapper - 1.16.0 - post processing update

  • Pulls in cgpCaVEManPostProcessing 1.9.0
    • Edgecase fix for overlapping reads - cause +1 variant at WGS scale (https://github.com/cancerit/cgpCaVEManPostProcessing/pull/36)
    • Major performance improvement (https://github.com/cancerit/cgpCaVEManPostProcessing/pull/37)

- Perl
Published by keiranmraine about 6 years ago

https://github.com/cancerit/cgpcavemanwrapper - 1.15.2 - Speed improvements via flagging

  • Upgrade to cgpCaVEManPostProcessing 1.8.9

- Perl
Published by over 6 years ago

https://github.com/cancerit/cgpcavemanwrapper - 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

- Perl
Published by over 6 years ago

https://github.com/cancerit/cgpcavemanwrapper - Hotfix - 1.13.4

- Perl
Published by kathryn-beal over 7 years ago

https://github.com/cancerit/cgpcavemanwrapper - Hotfix - 1.13.3

1.13.3

- Perl
Published by over 7 years ago

https://github.com/cancerit/cgpcavemanwrapper - Hotfix - 1.13.2

1.13.2

- Perl
Published by about 8 years ago

https://github.com/cancerit/cgpcavemanwrapper - 1.13.1 - Hotfix

1.13.1

- Perl
Published by over 8 years ago

https://github.com/cancerit/cgpcavemanwrapper - 1.13.0 - Overlapping read support

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

- Perl
Published by over 8 years ago

https://github.com/cancerit/cgpcavemanwrapper - 1.12.0 - Intermediate output gzipped

  • Use CaVEMan 1.12.0
  • Deal with CaVEMan 1.12.0 intermediate output now being gzipped

- Perl
Published by almost 9 years ago

https://github.com/cancerit/cgpcavemanwrapper - 1.10.3

Update CaVEMan dep to bring htslib version in line with CGP stack.

(1.10.2 replacement - Unused archive path in CaVEMan caused confusion on upgrade of htslib)

- Perl
Published by keiranmraine over 9 years ago

https://github.com/cancerit/cgpcavemanwrapper - 1.10.1 - correction to setup.sh

As 1.10.0, but fixes #28 and an error in setup.sh

- Perl
Published by keiranmraine over 9 years ago

https://github.com/cancerit/cgpcavemanwrapper - 1.10.0 - Update to faster CaVEMan core

  • Update default CaVEMan core to 1.11.0

Error in setup.sh, please use 1.10.1

- Perl
Published by over 9 years ago

https://github.com/cancerit/cgpcavemanwrapper - Bugfix release - 1.9.9

See: CaVEMan 1.9.5 release note

- Perl
Published by keiranmraine almost 10 years ago

https://github.com/cancerit/cgpcavemanwrapper - Bugfix release - 1.9.8

  • CaVEMan version 1.9.4

- Perl
Published by almost 10 years ago

https://github.com/cancerit/cgpcavemanwrapper - Bugfix release - 1.9.7

CaVEMan version 1.9.3

- Perl
Published by almost 10 years ago

https://github.com/cancerit/cgpcavemanwrapper - Feature Release - 1.9.0

  • CaVEMan core 1.8.0
  • Allows no flagging to occur but still complete - separate flagging process

- Perl
Published by over 10 years ago

https://github.com/cancerit/cgpcavemanwrapper - Bugfix release - 1.8.1

  • Minor syntax error was missed in 1.8.0

- Perl
Published by over 10 years ago

https://github.com/cancerit/cgpcavemanwrapper - Feature Release - 1.8.0

  • CaVEMan core now 1.8.0

- Perl
Published by over 10 years ago

https://github.com/cancerit/cgpcavemanwrapper - Bugfix release - 1.7.5

  • CaVEMan version upped to 1.7.2

- Perl
Published by over 10 years ago

https://github.com/cancerit/cgpcavemanwrapper - Bugfix Release - v1.7.4

  • CaVEMan core 1.7.1

- Perl
Published by over 10 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.7.2 - fix error in wrapper code

Changes to command line args in underlying code were missed.

- Perl
Published by keiranmraine almost 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.7.1 - Minor bugfixes

Includes change to base caveman algorithm to handle extreme numbers of readgroups.

- Perl
Published by keiranmraine almost 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.6.0

CaVEMan core version now 1.6.4 with several bug fixes included.

- Perl
Published by almost 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.5.2

Adding analysis process to flagging command.

- Perl
Published by almost 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.5.1 - install fix

Ensures mergeCavemanResults from CaVEMan is deployed.

- Perl
Published by keiranmraine about 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.5.0 - bugfixed caveman and support for BED based unmatched normal

v1.5.0: Pulls bugfixed version of CaVEMan 1.6.1 Supports BED version of caveman unmatched normal files.

- Perl
Published by keiranmraine about 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.4.1 - correct limit based processing

Number of required threads when using limit was not being set correctly. Generally results in needless thrashing of disk doing file checks but in some cases corrupt data or race conditions were occurring.

- Perl
Published by keiranmraine over 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.4.0 - pulldown flagging functional

Additional command-line options required to make pulldown (WXS) flagging work are added, should be used in conjunction with cgpCaVEManPostProcessing v1.1.0 or better

- Perl
Published by keiranmraine over 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.3.1 - as v1.3.0 with correct version reported

No other real changes, see v1.3.0

- Perl
Published by keiranmraine over 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - CaVEMan 1.5.2 and species/assembly behaviour altered

Bad version number, please use v1.3.1

- Perl
Published by over 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.2.0 - CaVEMan 1.5.1

Upgraded to CaVEMan 1.5.1 which uses htslib access methods to improve split step.

Minor code changes to handle incompatible fasta indexing between pre 1.0 samtools and htslib samtools.

- Perl
Published by keiranmraine over 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.1.3 - Updated underlying CaVEMan version

Other minor modifications are to allow certain dependancies to only be required when specific step is requested when '-p' is in use.

- Perl
Published by keiranmraine over 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - v1.1.2 - Stable release

Uses CaVEMan v1.4.2, allows http/ftp based normal panels and germline bed file is only required at the flag step when -process is specified.

- Perl
Published by keiranmraine over 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - Stable version, from dev branch, pre release - 1.1.1

Fixes #2 #5 #6 Updates to order of code in option setup to fix bug where job limit checking was throwing an error.

- Perl
Published by over 11 years ago

https://github.com/cancerit/cgpcavemanwrapper - Stable version, from dev branch, pre release - 1.1.0

This version was created to work with CaVEMan 1.3.n and above

- Perl
Published by almost 12 years ago

https://github.com/cancerit/cgpcavemanwrapper - Stable version, from dev branch, pre release - 1.0.0

Pre-release from dev of 1.0.0 which is compatible with CaVEMan 1.2.n and below. See later versions for later compatibility.

- Perl
Published by almost 12 years ago