v0.10.0

Changed

Read iterator now returns copies of alignments for more Pythonic behaviour.

v0.9.5

This version adds no user facing changes.

Fixed

• Pinned pip in Makefile so CI tests will run.

v0.9.4

Fixed

• Python source distribution did not include libdeflate directory.

v0.9.3

Added

• Linux and macOS ARM conda builds.

v0.9.1

Added

• --map_q command line option to filter reads by minimum mapping quality.

Fixed

• The default mapping quality was erroneously 1 not 0.

v0.9.0

Added

• "Other" modified base column to extended output. For example, when using
  -m 5mC to count 5-methylcytosine in reads, the "other" column will
  enumerate counts of other cytosine modifications present. When using the
  option --combine this column will contain zero (the counts being included
  in the modified base count).
• --theshold option to replace both -a and -b.

Fixed

• In line with the "other" column, when not using the --combine option
  the potential presence of other modifications in the same family of the
  base requested is taking into account. This has an effect of distributing
  some previously erroneous "canonical/non-modified" calls to "other" and
  "filtered" counts.

Removed

• The options -a and -b are deprecated. Instead use --threshold.

v0.8.0

Added

• --combine option to combine calls from all modified bases in a family.
  The previous behaviour was that the non-modified (canonical) count would
  have be incremented. For example when searching for 5mC modifications
  with -m 5mC and a 5hmC base was present, the read would contribute
  to the canonical count, not the modified count.

v0.7.0

Added

• --pileup option to output full raw base counts rather than BED methyl.

Changed

• -c no longer synonym to --cpg.
• ?-style MM subtags now handle correctly with "missing" entries being recorded
  as "no call" rather than implied canonical.
• extended output now includes a 15th column for "no call" bases.

Fixed

• Links in README.

v0.6.3

Changed

• Bumped htslib version to version 1.16 for fixes to MM tag parsing/validation.
• Change conda build back to bioconda::htslib since we're using a released version.

v0.6.2

Fixed

• Off-by-one in pointless BED field.