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XAM.jl
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61 Commits (develop)

Author SHA1 Message Date
Ciarán O'Mara 9a9f2c1f5a Fun with flags 
Implements flag queries.
 1 year ago
Ciarán O'Mara 0d1eec3ed3 Subtype from XAMRecord 1 year ago
Ciarán O'Mara 8151d877e7 Subtype from XAMReader and XAMWriter 1 year ago
Ciarán O'Mara 8272cea71e
Merge pull request #56 from jonathanBieler/bam_index_method 
Added method for handling different bam index types.
 2 years ago
Jonathan Bieler 286e271e91 update docstring 2 years ago
Jonathan Bieler 93a6b60d26 added method for handling different bam index types 2 years ago
Thomas A. Christensen II e6f542a368
Change alignment getter for BAM.Record to use existing cigar constructor 
Rather than keep a copy of the BioAlignments cigar constructor embedded in
this function, have it call the existing constructor. There may be
performance implications for using `cigar` instead of `cigar_rle`, but
having a second copy of the constructor here is an antipattern if I've ever
seen one, so prioritise stable code over performant code.
 2 years ago
Ciarán O'Mara 5da017052b Add messages to assertions 2 years ago
Ciarán O'Mara d37e9a04d8
Merge pull request #48 from MillironX/feature/BioAlignmentsv2.2 
Upgrade BioAlignments to v2.2 & BioSequences to v3
 2 years ago
Ciarán O'Mara 675e5828b1
Correct docstring 2 years ago
Thomas A. Christensen II a7a76db3d4
Update BAM.sequence to return BioSequences.LongDNA{4} 
Same principles apply as updating SAM.sequence
 2 years ago
Thomas A. Christensen II 1660a24a0f
Update SAM.sequence to return BioSequences.LongDNA{4} 
BioSequences v3 changed LongDNASeq to LongDNA{N}. We can't assume that
there aren't ambiguous nucleotides in a SAM file, so use the larger
LongDNA variant. The method signatures are also simplified, so simplify
their calls, accordingly.
 2 years ago
Jakob Nybo Nissen a72fcf47cb Improve documentation of flag function 3 years ago
Ciarán O’Mara 18dae0d45d Comments 3 years ago
Ciarán O’Mara 9d2a70531a Return early 3 years ago
Ciarán O’Mara 8f26bbf4a7 Tidy state machines and improve error messages 
Makes better use of the existing flow in [Automa.jl](b6997f7415/src/Stream.jl (L124-L127)).
 3 years ago
Ciarán O’Mara fa10f3bfcf Readability 3 years ago
Ciarán O’Mara 5bd793bc5f Merge branch 'master' into develop 3 years ago
Ciarán O’Mara c423694f29 Cater for blank sam files 3 years ago
Ciarán O’Mara 64f371e1e4 Adjust for Automa 0.8.1 
Defines an unambiguous state machine.
https://github.com/BioJulia/Automa.jl/pull/49.
 3 years ago
Jakob Nissen b086fefbd5 Make BAM record layout match BAM specs 4 years ago
Ciarán O'Mara d38c2becf0 Minimal adjustements 4 years ago
Jonathan Bieler dde235fbc8 improve BAM.quality performance 4 years ago
Ciarán O'Mara dce44b3f55 Tidy 4 years ago
Ciarán O'Mara 69e77a234c Note 4 years ago
Diego Alvarez 639b8238c7 Correct scope 4 years ago
Ciarán O'Mara 6141d679e8 Use `copyto!` 
https://github.com/BioJulia/BioSequences.jl/pull/95
 4 years ago
Ciarán O'Mara 946068b2f3 Simplify use of `appendfrom!` 4 years ago
Ciarán O'Mara 436cfd84ba Use @info 4 years ago
Ciarán O'Mara 73de48e232 Move imports 4 years ago
Ciarán O'Mara 81dbf41798 Merge branch 'master' into develop 4 years ago
Ciarán O'Mara 8b7a2ecc2b Correct not found check 4 years ago
Ciarán O'Mara 32a2b129e1 Merge branch 'master' into develop 4 years ago
Ciarán O'Mara f00547177f Empty records during iteration 4 years ago
Ciarán O'Mara 300158dbef Record equivalency functions 4 years ago
Ciarán O'Mara af675a2371 Merge branch 'master' into develop 4 years ago
Ciarán O'Mara 3e1a802372 Ensure fields are empty 4 years ago
Ciarán O'Mara aec919c713 Use unsafe copy 4 years ago
Ciarán O'Mara 429f69d84b Merge branch 'master' into develop 4 years ago
Ciarán O'Mara d0e2560ec4 Correct header parsing 4 years ago
Ciarán O'Mara e69c6de586 Equality comparators 4 years ago
Ciarán O'Mara cc2af1976b Use broadcast 4 years ago
Ciarán O'Mara 08e253c297 Use collect 4 years ago
Ciarán O'Mara de56faf066 Migrate from BufferedStreams to TranscodingStreams 4 years ago
Ciarán O'Mara 12db2c4ea8 Align emission symbols for TranscodingStreams 4 years ago
Ciarán O'Mara 6cd89aba08 Move isinteractive into machine 4 years ago
Ciarán O'Mara 892ad0d7dc Pipe into eval 4 years ago
Ciarán O'Mara e63ce2e398 Group Automa into readrecord.jl 4 years ago
Ciarán O'Mara 365f7922fa Quick fix for BioGenerics.ReaderHelper functions 
This fix is likely to be replaced when migrating to TranscodingStreams.
 4 years ago
Ciarán O'Mara c59a157675 Quick fix for BioCore.Ragel.State 
This fix is likely to be replaced when migrating to TranscodingStreams.
 4 years ago