v0.1.8

Changes

• [call-mods] Emit 0 ML value when a mod code is not called, previously the call was omitted (only the called mod was emitted).

Adds

• [adjust-mods, call-mods, pileup, sample-probs, summary, extract] Allow --edge-filter that will remove base modification probabilities at the ends of reads.

Fixes

• [call-mods] --no-filtering flag properly handled.

Deprecated

• [adjust-mods] In order to allow --edge-filter without also performing an ignore or convert, in the next release --ignore will require a explicit argument (h is no longer the default). In this release, when no edge filter, conversion, or ignore is provided, h will be used for ignore, but this behavior will be removed in the next release.

v0.1.7

Changes

Adds

• modkit extract sub-command that produces a table of per-read base modification probabilities.
• Allow suppression of progress bar with --suppress-progress

Fixes

• Don't count skipped reads towards total when sampling.

N.B.

modkit call-mods has a bug in this release where --no-filtering is not handled properly (filtering is still performed). Use a later release or as a work-around use --filter-threshold 0.0.

v0.1.6

Changes

• When ignoring a base modification in pileup, calculate pass thresholds on the probabilities after ignoring the specified probability.

Adds

• [pileup] API to specify pass thresholds per base modification (or canonical) with --mod-threshold option.
• New modBAM->modBAM subcommand, call-mods that will apply pass thresholds and clamp base modification probabilities to zero (canonical) or 1.0 for base modifications
• [sample-probs, summary] Allow --ignore to remove a base modification class from the analysis.

v0.1.5

Changes

• Table output is default in modkit summary, columns are all_counts/frac and pass_counts/frac instead of counts/frac and filt_counts/frac. See help for details.

Fixes

• The modkit summary command will not use all of the reads in the input modBAM when the --no-filtering flag is used. To disable sampling (and use all of the reads) use --no-sampling. See docs for details.

Adds

• The sample-probs command will now output histograms of the base modification probabilities with the --hist option.
• "Book-style" docs.

v0.1.4

Changes

• Implicitly canonical mode (., see SAM tags) does not require --force-allow-implicit. However no mode at all still does.
• modkit adjust-mods will allow conversion of base modification codes that aren't in the specification (e.g. Z). In order to process these with modkit pileup you must first run modkit adjust-mods in.bam out.bam --convert Z m (for example).
• Per-canonical base thresholds will be automatically inferred, e.g. different thresholds will be chosen for A mods and C mods. This is also true for modkit summary and modkit sample-probs.
• modkit summary will now allow specification of a --region when using an indexed BAM and will sample evenly over the aligned contigs when the region is omitted.

Adds

• modkit summary has --table option that produces a human-readable table.

Deprecated

• modkit summary tab-separated format will not be default in the next release. The table output (currently specified with the --table option will become the default).

Fixes

• Restructuring of the code allows for more parallelism when estimating threshold values, speeding up this process at the start of modkit pileup or modkit summary.

v0.1.4-rc1

Changes

• Filter base modification calls that are < the threshold value instead of <= the threshold value.

v0.1.3

Adds

• --mask flag in pileup and motif-bed

Fixes

• Default behavior will find CGs in masked regions of the reference.

v0.1.2

Adds

• First release.

Fixes