CHANGES.md

In mdraminski/CytoMeth: CytoMeth

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

mdraminski/CytoMeth documentation built on April 24, 2023, 4:09 a.m.