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v0.19.0 - Various fixes and improvements
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@FelixKrueger FelixKrueger released this 13 Oct 13:59
· 498 commits to master since this release
0.19.0
f20b2ec

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.

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.

deduplicate_bismark

  • Added option --multiple to the deduplicator to treat several input SAM/BAM files as the same sample. Here is issue #107.

  • Added option --output_dir to deduplicate_bismark so that it can be used in the Google cloud. Here is issue #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 <int> 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.

  • 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

copy_files_for_release

  • Is now working from any location.
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