diff --git a/CHANGELOG.md b/CHANGELOG.md index 62fa146..0ec7fc2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,10 @@ ## Changelog for Bismark v0.18.2_dev +### Bismark + +Changed the methylation call behaviour so that insertions in a read (which are filled in with `X` for the methylation call) are also considered as `Unknown context` for the methylation call. Here is [issue#135](https://github.com/FelixKrueger/Bismark/issues/135). + ### filter_non_conversion Added new options `--percentage_cutoff [int]` and `--minimum_count [int]` to allow filtering reads for non-bisulfite conversion using an overall methylation percentage and count cutoff. Here is [issue #122](https://github.com/FelixKrueger/Bismark/issues/122). @@ -10,14 +14,39 @@ Added new options `--percentage_cutoff [int]` and `--minimum_count [int]` to all Added option `--multiple` to the deduplicator to treat several input SAM/BAM files as the same sample. Here is [issue #107](https://github.com/FelixKrueger/Bismark/issues/107). -Added option `-output_dir` to `deduplicate_bismark` so that it can be used in the Google cloud. Here is [issue #123](https://github.com/FelixKrueger/Bismark/issues/123) +Added option `--output_dir` to `deduplicate_bismark` so that it can be used in the Google cloud. Here is [issue #123](https://github.com/FelixKrueger/Bismark/issues/123) ### coverage2cytosine +Output files are now handled better and more consistently. Default processing now produces the following output files (with `--gzip`): +``` +CpG_report.txt(.gz) or +CX_report.txt(.gz) +``` + +The option `--NOMe-Seq` now produces four output files (with `--gzip`): + +``` +NOMe.CpG_report.txt(.gz) +NOMe.CpG.cov(.gz) +NOMe.GpC_report.txt(.gz) +NOMe.GpC.cov(.gz) +``` +The option `--split_by_chromosome` should work in either default, `--gc` or `--NOMe-seq` mode. + +NOMe-Seq processing if now ignoring processing that were not covered by any reads. + Improved handling of the `--output_dir`, i.e. the folder will be created if it doesn't exist already and making the path absolute. Added new option `--discordance ` to allow filtering for discordance pf top and bottom strand when in `--merge_CpG` mode. CpG positions for which either the top or bottom strand was not measured at all will not be assessed for discordance and hence appear in the regular 'merged_CpG_evidence.cov' file. More details in [issue #91](https://github.com/FelixKrueger/Bismark/issues/91). +Fixed context extraction for Gs at positions 1 and 2 of a chromosome/contig. Also, last cytosine positions of not covered chromosomes are now ignored in the same way as for covered chromosomes [issue #127](https://github.com/FelixKrueger/Bismark/issues/127) + +### copy_files_for_release + +Is now working from any location. + + ## Changelog for Bismark v0.18.2 ### Bismark