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CytoMeth - Changes

Version 1.0.3

  • fixed CytoMethQC script - now all data is loaded from rds results files

Version 1.0.2

  • samtools is used for sorting (multithreaded)

Version 1.0.1

  • more than one control is now available

Version 1.0.0

  • added BS-Snper tool that provides methylations and SNP
  • adjusted start/end positions in the output .bed file
  • fixed some minor issues
  • updated documentation

Version 0.9.21

  • minor updates
  • updated documentation

Version 0.9.20

  • updated reference files
  • updated documentation

Version 0.9.19

  • new parameter in config file methratio_processing
  • bunch of fixes and improvements

Version 0.9.18

  • some rare issues in exporting to bed file fixed
  • improved continuation of calculation after the stop
  • logging on the screen improved

Version 0.9.17

  • param java_mem is now memory
  • BSMAP uses I parameter (automatically set up based on available memory)
  • manual updated

Version 0.9.16

  • bam files can be used as an input
  • less memory usage during CalcMethylation Step

Version 0.9.15

  • reshape2 fix
  • updated Dockerfile and install.packages.R files
  • autodetect total memory size and cpu cores and fix the config if needed
  • reference data directory change
  • manual updated

Version 0.9.14

  • new plot functions plotSitesCpG and plotSitesNonCpG allow for any min_coverage
  • manual updated

Version 0.9.13

  • output files bed format - finalized structure
  • new output files rds format

Version 0.9.12

  • generation of QCSummary is now independet process
  • plot plotBetaValuesSummary supports data sampling and non-CpG context
  • new config parameter 'ref_control_sequence_name'
  • plots updated

Version 0.9.11

  • new fontsize parameter in plots

Version 0.9.10

  • picard updated
  • tools.conf.yml updated
  • readme file updated and extended
  • output files section in readme file updated and extended

Version 0.9.9

  • picard updated
  • checking of log files updated

Version 0.9.8

  • README updated
  • QC extended
  • install.packages.R extended by bioconductor packages
  • Dockerfile added
  • install.data.sh added

Version 0.9.7

  • README updated
  • FastQC QC report creation added
  • trimmomatic_MINLEN parameter added
  • seqtk added

Version 0.9.6

  • GATK version 3.8.1
  • improved error handling and missing file checking
  • improved skipping of already calculated phases
  • improved README
  • methratio.py fixed and added (-X removed)

Version 0.9.5

  • first GitHub Version
  • installation process install.sh file
  • picard version 2.20.1 integrated
  • conda integration - all non Java tools installed by conda
  • tools.conf.yml added
  • README.md and CHANGES.md files added