v0.4.1

Adds

• [docs] Fix documentation links
• [dmr] Address bug where assert fires when one sample does not have any records over a region, fixes #265A

Fixes

• [sample-probs] Add arguments to specify the colors of the histogram output, also make them deterministic when not given
• [summary] Make table ordering deterministic.

v0.4.0

Adds

• [motif] Add search and evaluate subcommands under motif command hierarchy.
• [stats, localize] Add stats and localize commands, see documentation for details.
• [dmr, multi] Combine samples when they have the same name.
• [extract] Add option to emit bgzf-compressed output.

Fixes

• [validate] Only consider modification codes attributed to the primary sequence base being validated.
• [pileup, extract] Improve iteration over regions when --include-bed is provided.

Changes

• [dmr] Use htslib tbx module for reading tabix index instead of noodles.
• [pileup] Require .fai FASTA index when a reference is provided, load only sections of reference that are necessary.
• [extract] Separate calls and full commands to produce the read calls, and full tables, respectively.
• [validate] Change "any-mod" code from {A, C, G, T} to *.

v0.3.3

Fixes

• [sample-probs, summary, pileup] Refactor sampling algorithm so that it will not over-sample reads leading to excessive memory usage.
• [validate] Only use modifications on the canonical base we're validating (in case the modBAM has multiple, e.g. A and C-mods).
• [entropy] Check that reference sequences are the same as in the bam header

v0.3.2

Fixes

• [thresholds] OOB panic fix, #244
• [dmr, pair] Allow strand information in regions to be provided. #240
• [dmr, multi] Fix problem when many pairs are provided (#229)

Adds

• [sample-probs] Change output format of probabilities table to make it easier to parse, also change schema. Output HTML documents with nicer tables.
• [ci] Build in Ubuntu-16 due to Centos7 EOL.

v0.3.1

Fixes

• [call-mods] Always change model to "explicit", dropped base modification probabilities should not be interpreted as canonical.
• [dmr, segment] Add pseudo-count to avoid -inf in HMM.
• [find-motifs] Fix crash in exhaustive search.

Adds

• [dmr] Allow specification of mod code-to-primary base on the command line with --assign-code.

v0.3.1rc1

Fixes

• [find-motifs] Bug where error would be reported when output tables are specified. Fixes #195

Adds

• [extract] Allows streaming read calls table directly to stdout.

v0.3.0

Fixes

• [validate] Fix bug where observations were not being balanced correctly.
• [dmr] Revert noodles to 0.50.0, partially fixes #178.

Adds

• [find-motifs] Add command to find motif sequences that are enriched for base modification.
• [entropy] Add command to calculate methylation entropy.
• [dmr] Add --segment option to categorize modified positions into contiguous "same" and "different" groups.
• [pileup] Add --header option to emit a column header.

Deprecations

• [pileup] Change output to always be all-tab delimited, next version will error with --only-tabs flag.

v0.2.8-rc1

Fixes

• [dmr] Don't crash when using matched samples, but not all samples have modification counts at a position. Fixes #165.
• [update-tags] Correctly handle implicit tags when there are no probs, i.e. C+h -> C+h.., fixes #160.

v0.2.7

Fixes

• [dmr] Header was incorrect with multiple samples
• [pileup] Improve performance when using --include-bed, only process contigs in the BED file.
• [dmr, single-site] When using multiple samples, don't fail a position when one or more samples doesn't have a modification call at that position.
• [extract] Expose queue size to reduce memory usage with long reads.
• [validate] Report number of calls filtered out with thresholds.

v0.2.6

Fixes

• [dmr, single-site] Don't require that there are equal numbers of samples for single site DMR with multiple samples. Fixes #140.
• [dmr, pairwise, region] Protect when zero bedmethyl records are found for a region, fixes #146.

Adds

• [validate] Adds on-the-fly filtering of reads by alignment identity and/or alignment length.