millironx/XAM.jl
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139 commits 21 branches 10 tags 2.5 MiB
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20 commits

Author SHA1 Message Date
Ciarán O'Mara
560a5cd8df Check that EOF_BLOCK gets written 2023-05-02 14:56:48 +10:00
Ciarán O'Mara
8272cea71e
Merge pull request #56 from jonathanBieler/bam_index_method 
Added method for handling different bam index types.
 2022-10-14 22:15:31 +11:00
Jonathan Bieler
93a6b60d26 added method for handling different bam index types 2022-10-13 15:06:39 +02:00
Thomas A. Christensen II
f7b9d9fa75
Update tests to use new AlignmentAnchor structure 2022-10-10 16:24:26 -05:00
Ciarán O'Mara
8424757cc2 Merge branch 'master' into develop 
# Conflicts:
#	Project.toml
#	test/runtests.jl
 2022-08-15 15:34:24 +10:00
Ciarán O'Mara
99aa013c2b Add tests for issue #31 
Test for expected results as described in https://github.com/BioJulia/XAM.jl/issues/31.
 2022-08-15 12:30:27 +10:00
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)).
 2021-06-29 13:25:30 +10:00
Ciarán O’Mara
c56eb0851a Update Continuous Integration workflows 
- Includes doctest in tests.
 2021-06-29 13:23:00 +10:00
Ciarán O’Mara
5bd793bc5f Merge branch 'master' into develop 2021-04-01 12:37:54 +11:00
Ciarán O’Mara
c423694f29 Cater for blank sam files 2021-04-01 12:37:35 +11:00
Jakob Nissen
b086fefbd5 Make BAM record layout match BAM specs 2020-10-20 01:52:31 +11:00
Ciarán O'Mara
433b8d14e8 Begin crosschecks 2020-08-13 16:45:51 +10:00
Ciarán O'Mara
0ac352f1d2 Isolate testsets 2020-06-20 23:31:45 +10:00
Ciarán O'Mara
5fa8c5bd2e Tests for in-place-reading pattern 2020-04-17 15:51:11 +10:00
Ciarán O'Mara
f6846edfb1 Check header in roundtrip 2020-03-21 17:16:14 +11:00
Ciarán O'Mara
c4f3c4b0df Migrate to BioGenerics 
Basic find and replace.
 2020-03-13 23:01:25 +11:00
herbstk
6a33ac06a7 ✅ Enhanced unit test for rightposition (#37) 
Added additional tests for SAM.Record and BAM.Record for `rightposition` (and implicitly `alignlength`).
 2020-03-13 20:41:06 +11:00
Ciarán O'Mara
2df146b8fc Use FormatSpecimens 2020-02-26 10:28:39 +11:00
Ciarán O'Mara
1a3c986152 Minimal code adjustments for working separation 
- Update to use GenomicFeatures v2.
- BioAlignments v2.
- BioSequences v2.
- Indexes v0.1.
 2020-02-20 21:19:07 +11:00
Ciarán O'Mara
7a56931b90 Naive code roundup 2020-02-20 10:19:28 +11:00