Release/v0.4.0 - Githubissues

BioJulia / XAM.jl

Parse and process SAM and BAM formatted files

MIT License

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Release/v0.4.0 #66

Closed CiaranOMara closed 8 months ago

CiaranOMara commented 8 months ago

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.

CiaranOMara commented 8 months ago

@jakobnissen, I think your comments can be resolved, and this is ready for another check. I have attempted to align the nomenclature with the SAM spec. So, it should be more consistent. Though, I'm unhappy about the method isproperpair and associated variables, as there can be more than two segments in a template - Do you have any ideas?