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.

v0.1.13

Fixes

• [extract, mod_bam] Potential stack overflow when many reads are skipped.
• [extract] Output inferred canonical calls when the . MM tag is used.
• [adjust-mods] change MM flag to ? and add inferred canonical calls when --edge-filter is applied.

Adds

• [pileup] performs pileup in batches to decrease peak memory usage, configurable with --chunk_size.
• [pileup] Allow users to narrow output to any number of specified motifs (instead of only CpG dinucleotides) with --motif option

Changes

• [extract] adds inferred column

v0.1.13-rc1

Fixes

• [extract, mod_bam] Potential stack overflow when many reads are skipped.

v0.1.12

Fixes

• [extract] no longer requires an index to use --num-reads, it will just take the first --num-reads reads if no index is found.

Adds

• New command, modkit repair allows projecting base modifiction calls from one modBAM onto another where the reads have beem trimmed or clipped.
• adjust-mods, update-tags, sample-probs, summary, call-mods and extract can now be used with standard input/output streams.

v0.1.11

Fixes

• [extract] Correctly handles duplex modBAMs when using --include-bed
• Refactors handling of CRAM when sampling records. Fixes #35. Suggests to use BAM.

Adds

• [extract] Output contains ref_mod_strand and modified_primary_base
• [pileup] New option --max-depth allows increasing depth beyond default in hts-lib and sets the default to 8,000 in case it changes in hts-lib.

v0.1.11-rc1

Fixes

• [extract] Correctly handles duplex modBAMs when using --include-bed

v0.1.10

Fixes

• Don't log message whilst aggregating base modification probabilities (exposed with duplex reads as input).

Changes

• [pileup] Fail fast when bam index doesn't contain any mapped reads.

v0.1.9

Changes

• [pileup] When estimating the pass-threshold only use base modification probabilities if the read base is aligned to the reference (don't use soft-clipped and inserts). Use --include-unmapped to use all base modification probabilities.
• [adjust-mods] requires --ignore, --convert, or --edge-filter.

Adds

• [pileup, extract, sample-probs, summary] Allow narrowing of analysis to specific sites with --include-bed.
• [summary, sample-probs] Add --only-mapped flag that will only report on base modification probabilities if they are mapped to the reference.
• [pileup] Allow partitioning counts to separate bedMethyl files based on SAM tags with --partition-tag option.

Fixes

• [adjust-mods, update-tags, call-mods] Panic when failure to parse SAM header, fixes #29.