v0.2.5

Fixes

• [extract] Only emit mapped reads when --region is provided, but still emit unmapped bases in those reads unless --mapped-only is passed.
• [extract] Performance improvement due to better tracking of interval boundaries.
• [repair] Updates the MN tag on repaired records.

Adds

• [dmr, single-site] Refactor dmr pair without regions (i.e. single site analysis) to increase performance.
• [dmr, single-site] Add estimated MAP-based p-value to output.
• [all] Allows BED3 input for all options that use --include-bed. Strand will be assumed to be BOTH (equivalent to '.').
• [extract] Increases the kmer size limit to 50.

v0.2.5-rc2

Fixes

• [all] Reads with entirely implicit canonical calls are no longer skipped for "modbase info empty" or similar.

Adds

• adds the --no-implicit-calls flag to modkit update-tags so when changing from the "probability of modification" modes (".", and "") to explicit mode (?) implicit cannonical calls can be skipped. This is important, for example, if the modification calling model did not have the ? mode available.

v0.2.5-rc1

Adds

• modkit validate sub-command for rigorous testing of modified base calling models when ground truth labels are known.

Fixes

• [all] Improve performance when using commands on transcriptome reference (or any reference with many sequences less than ~100kb).

v0.2.4

Adds

• [extract, adjust-mods, update-tags, call-mods] Parse MN tag in order to use secondary and supplementary alignments.

Fixes

• [all] Improve performance slightly when using short and frequent motifs with --motif option.

v0.2.3

Adds

• [dmr, multi] Allow site-level scoring by omitting the --regions argument. Sites will be collected from the input bedMethyl files.
• [dmr] Friendlier handling of missing files and when regions aren't found in the bedMethyl input files.
• [dmr] allow filtering on valid coverage without changing input
• [extract] output "read calls" extract table, a TSV with the base modification calls for every modified position in every read using the same thresholding algorithm as pileup
• [extract] allow filtering of calls by reference motif (like in pileup) as well as BED regions (and exclude regions)

Fixes

• [extract] Improve performance, especially on longer reads.
• [extract] Improve performance with long reads (actually a bug fix)
• [extract] num_soft_clipped_start and num_soft_clipped_end were incorrect on some reverse-mapped reads

v0.2.3-rc1

Adds

• [dmr, pair] Allow site-level scoring by omitting the --regions argument. Sites will be collected from the input bedMethyl files.
• [dmr] Friendlier handling of missing files and when regions aren't found in the bedMethyl input files.

Fixes

• [extract] Improve performance, especially on longer reads.

Changes

v0.2.2

Adds

• [all] Allow ChEBI codes and more flexible single-character modification codes. E.g. now you can use c for carboxy cytosine or z for something exotic.
• [extract] Adds --kmer-length option to modulate the kmer length on the command line.

Fixes

• [dmr] Automatically select the correct bedMethyl rows when using multiple modified bases (e.g. C-mods and A-mods). Removes assert and replaces it with a warning.

Deprecated

• In the next version pileup output will only have tab delimiters and the --only-tabs flag will be removed.

v0.2.2-rc1

Fixes

• [logging] Changes log level from error to debug when a record doesn't have any base modification probabilities.

v0.2.1

Adds

• [adjust-mods, summary, pileup, call-mods] Allows asymmetric edge filter (i.e. filter out base modification calls X bases from the start of the reads and Y bases from the ends). Previously, only one parameter was allowed and filtering was symmetric.

Fixes

• [summary, sample-probs] Fixes bug where inferred canonical bases were not being accounted for.
• [dmr] Fail when cannot parse any bedMethyl lines from input, log when there are failures to parse lines, fixes #60
• [dmr] Automatically make directory if it doesn't already exist, fixes #61

v0.2.0

Adds

• [dmr] Adds modkit dmr command suite for differential methylation exploratory data analysis.
• [pileup-hemi] Adds modkit pileup-hemi for tabulating double-stranded methylation patterns.

Fixes

• [repair] Fixes potential stack overflow when donor and/or acceptor BAMs aren't sorted correctly.