Version 1.2.1

Improved CpG counting per target interval.
Added read downsampling prior to conversion rate calculation.

Version 1.2.0

Fixed handling of aggregate values over genomic intervals to include CpGs ignored during extraction due to coverage/SNP filter.
Added DMR annotation with closest gene using bedtools closest.
Added empty table handling in R to stop when no positions pass filtering or no differentially methylated regions are detected.
Added path to Rlib containing required libraries.

Version 1.1.0

Fixed bugs in trimReads in user mode.
Updated memory limits to avoid jobs being killed by slurm controller. Restricted nodes per task to 1 to avoid spreading of tasks over nodes.
Implemented multithreaded cutadapt version.
Replaced read group info adding with picard by passing the information to bwa meth at the alignment step.
Replaced PCR duplicate removal with picard by sambamba.

Version 1.0.1

Added version parsing and forwarding to R commands, Rpath passing to R commands.

Version 1.0.0

This is a light pipeline version, starting from sequencing reads. Auto or user-directed read trimming is performed. Reads are mapped to a reference genome stored in local repo with bwa-meth, MethylDackel is used for methylation extraction, and metilene for DMR colling. Single cytosine as well as genomic interval aggregate stats are performed with limma on logit-transformed beta values. A quality report with bisultfite coversion rates, mapping rates, coverage and methylation bias is produced.

Version 0.0.3

v0.0.3

fixes in the lite version

Version 0.0.2

v0.0.2

user guide added