v0.6.1

Fixes

• [pileup] Fix combine strands when falling back to 'generic workers' fixes #545
• [pileup] Use bgzf compression when falling back to 'general workers', fixes #556
• [pileup] Fix bug in --phased when only one modification is requested fixes #552
• [pileup] Only emit 5hmC or Inosine records when these are the only base modifications requested, fixes #555
• [pileup] Use default threshold for all bases without specific threshold, fixes #564
• [pileup] Saturating add at high depth and add --high-depth flag, fixes #547
• [adjust] Actually add CG 0 when --cpg flag is passed, fixes #502
• [bedmethyl, tobigwig] Allow header in bedmethyl input thanks @WardDeb
• [motif, search] Change comparison logic so that it compares the sequence set represented by the motifs, fixes #553

Adds

• [pileup] Add --bedrmod flag to output bedRMod headers

v0.6.0

Changes

• [pileup] refactor pileup to increase efficiency. See migration guide and limitations for details.

v0.5.1-rc1

Fixes

• [pileup] Fixes bug where N_diff was incorrectly summed when --combine-strands was used. (N.B. %-methylation was still correct).
• Fixes bug where fallback threshold was incorrect. Will now be highest observed explicit canonical probability, was highest bin.
• Fixes conversion to bigWig when chromosomes aren't sorted exactly the way that sort would do it.

Adds

• [cli] Adds shell completions command, thanks to @killercup
• [dmr] Adds 2OMe mod codes
• [validate] Adds better logging when NM tag is missing or reads fail.
• Allows bgzip-compressed FASTA references across all commands
• [bedmethyl, tobigwig] Allow using header from modBAM instead of sizes.

v0.5.0

Adds

• [open-chromatin] Adds open chromatin prediction subcommand for 6mA MTase-treated DNA
• [all] Fallback to ML 254 when threshold is estimated as 1.0

Changes

• [all] Refactor to workspaces
• [modbam, check-tags] Adds --head <n> option to take first n reads

Fixes

• [stats] Allow BED5 input regions and header/comment lines

v0.4.4

Adds

• [extract] Adds alignment start and end columns
• [extract] Adds motif annotation column
• [localize] Allow BED4 input regions
• [dmr] Improve logging and error reporting, adds --careful to output table of contigs that can be processed.
• [dmr] Adds Cohen's h statistic
• [motif, search] Adds "batch and narrow" exhaustive search algorithm
• [motif, search] Adds structured logging

Changes

• [all] Any output that is BED-like will have headers with "#" comment symbol
• [dmr] Change maximum allowed coverage in MAP-based p-value from 300 to 100.

Fixes

• [all] Correctly parse "transcript"-like contigs for --region arguments
• [dmr] Correctly handle bedMethyl tables with multiple motifs in the name column

Documentation missing
This build comes with documentation (a manual) that is missing the description of Cohen's h statistic in the DMR output. The online version of the manual has been updated.

Changelog missing

• [dmr] Change maximum allowed coverage in MAP-based p-value from 300 to 100.

Is not present in the tagged version of the Changelog.

v0.4.4-rc1

Fixes

• [bedmethyl, merge] Merge and write concurrently, improves memory usage and runtime massively.
• [dmr] Don't fail an entire section (i.e. batch) when one sample does not have a particular contig.
• [modbam, check-tags] Fix counter so that records that fail reading are counted.
• [pileup, sampler] Don't use non-primary alignments when calculating pass thresholds.

v0.4.3

Adds

• [bedmethyl] Extract bigWig tracks from bedMethyl files
• [modbam] check-tags command to validate MM/ML tags
• Allow "generic" MM tags
• Add error-tabulation table to most commands

Fixes

• [sample-probs] Make colors the same in the output charts (fixes #345).
• [bedmethyl, merge] Perform an outer join as stated in the documenttion (fixes #334).
• [pileup] BAM-header ordering of contigs when using --include-bed

v0.4.2

Adds

• [entropy] Entropy can now be calculated with multiple motifs and multiple modified primary bases.
• [adjust-mods, call-mods] Retain or remove base modification calls based on whether they match a sequence motif in the basecall sequence.
• [bedmethyl] Add command to merge bedMethyl files.
• [dmr] Add strand to DMR output.

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 *.