Changelog

All notable changes to XAM.jl will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Added conversion capability for SAM to BAM (#63).

0.4.0

Added

Added BAM.Reader index support for BAI object (#56).
Added doi badge.
Added test to ensure EOF_BLOCK gets written.
Added isreversestrand.
Added isfirstsegment.
Added islastsegment.

Changed

Subtype from XAMReader and XAMWriter from common abstract types.
Subtype from XAMRecord.
Unified flag queries.
Improved Slack link.
Updated to use Automa v1 (#65).
Pointed the Unit Tests badge at the develop branch.
Pluralised flag.
Renamed ismateunmapped to isnextunmapped.
Renamed isreverse to isreversecomplemented.
Renamed isforward to isforwardstrand.
ispositivestrand aliases isforwardstrand.
isnegativestrand aliases isreversestrand.
Renamed ismatereverse to isnextreversecomplemented.
isread1 aliases isfirstsegment.
isread2 aliases islastsegment.

Fixed

Updated hts-files.md (#62).
Corrected the behaviour of isprimaryalignment with isprimary.

Removed

Moved the functionality of isprimary into isprimaryalignment.

0.3.1

Changed

Upgraded to BioAlignments v3 (#55).

0.3.0 - 2022-10-10

Added

Crosschecks for SAM and BAM (#29).
Improved documentation for flags (#43).

Changed

BAM.quality performance improved (#21).
Updated BioAlignments to v2.2 and BioSequences to v3 (#48).

Fixed

BAM.Record layout now matches the BAM specs (#26).