millironx/XAM.jl
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Author SHA1 Message Date
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
fa10f3bfcf Readability 2021-06-29 13:23:00 +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
22667dc7af Merge branch 'hotfix/issue-34' 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
Ciarán O’Mara
64f371e1e4 Adjust for Automa 0.8.1 
Defines an unambiguous state machine.
https://github.com/BioJulia/Automa.jl/pull/49.
 2021-04-01 12:37:35 +11:00
Ciarán O’Mara
aaf3710fbe Increment version 2021-03-27 00:28:44 +11:00
Jakob Nissen
b086fefbd5 Make BAM record layout match BAM specs 2020-10-20 01:52:31 +11:00
Ciarán O'Mara
8836b4dbb6
Merge pull request #29 from CiaranOMara/feature/crosscheck 
Begin crosschecks
 2020-10-20 01:50:13 +11:00
Ciarán O'Mara
d38c2becf0 Minimal adjustements 2020-08-13 16:45:53 +10:00
Ciarán O'Mara
433b8d14e8 Begin crosschecks 2020-08-13 16:45:51 +10:00
Jonathan Bieler
dde235fbc8 improve BAM.quality performance 2020-08-02 17:40:52 +10:00
Ciarán O'Mara
dce44b3f55 Tidy 2020-07-08 23:30:44 +10:00
Ciarán O'Mara
69e77a234c Note 2020-07-08 23:30:44 +10:00
Ciarán O'Mara
a51e91141f Merge branch 'hotfix/isnextmapped' 2020-07-08 23:06:44 +10:00
Ciarán O'Mara
149d2cd898 Merge branch 'master' into develop 2020-07-08 23:06:44 +10:00
Diego Alvarez
639b8238c7 Correct scope 2020-07-08 11:57:31 +10:00
Ciarán O'Mara
eb11106b01 Increment version 2020-07-08 11:03:10 +10:00
Ciarán O'Mara
dfa5a3217f Merge branch 'release/v0.2.5' 2020-06-22 10:48:03 +10:00
Ciarán O'Mara
b97c97e90f Merge branch 'master' into develop 2020-06-22 10:48:03 +10:00
Ciarán O'Mara
bde477d54f Increment version 2020-06-22 10:35:34 +10:00
Ciarán O'Mara
6141d679e8 Use copyto! 
https://github.com/BioJulia/BioSequences.jl/pull/95
 2020-06-22 10:30:51 +10:00
Ciarán O'Mara
946068b2f3 Simplify use of appendfrom! 2020-06-22 10:30:51 +10:00
Ciarán O'Mara
436cfd84ba Use @info 2020-06-20 23:32:01 +10:00
Ciarán O'Mara
73de48e232 Move imports 2020-06-20 23:31:53 +10:00
Ciarán O'Mara
0ac352f1d2 Isolate testsets 2020-06-20 23:31:45 +10:00
Ciarán O'Mara
eaf5c73eb5 Update CI and documentation for the general registry 
- Update documentation workflow.
- Update CompatHelper workflow.
- Update TagBot workflow.
- Update unit test workflow.
- Update codecov.
 2020-06-20 23:31:02 +10:00
Ciarán O'Mara
81dbf41798 Merge branch 'master' into develop 2020-05-22 13:03:58 +10:00
Ciarán O'Mara
551a5906c5
Merge pull request #12 from BioJulia/hotfix/iterate 
hotfix/iterate
 2020-05-22 12:53:43 +10:00
Ciarán O'Mara
8b7a2ecc2b Correct not found check 2020-05-22 12:12:37 +10:00
Ciarán O'Mara
cc18311539 Increment version 2020-05-22 12:12:37 +10:00
Ciarán O'Mara
32a2b129e1 Merge branch 'master' into develop 2020-04-18 00:26:14 +10:00
Ciarán O'Mara
060349bd2b Merge branch 'hotfix/iteration' 2020-04-18 00:26:14 +10:00
Ciarán O'Mara
b440bc3c4d Update documentation 2020-04-17 15:56:23 +10:00
Ciarán O'Mara
f00547177f Empty records during iteration 2020-04-17 15:56:23 +10:00
Ciarán O'Mara
300158dbef Record equivalency functions 2020-04-17 15:56:23 +10:00
Ciarán O'Mara
5fa8c5bd2e Tests for in-place-reading pattern 2020-04-17 15:51:11 +10:00
Ciarán O'Mara
bb13a38cf7 Increment version 2020-04-17 15:49:24 +10:00
Ciarán O'Mara
af675a2371 Merge branch 'master' into develop 2020-04-12 17:35:21 +10:00
Ciarán O'Mara
0e0908f985 Merge branch 'hotfix/memory' 2020-04-12 17:35:21 +10:00
Ciarán O'Mara
3e1a802372 Ensure fields are empty 2020-04-12 17:35:01 +10:00
Ciarán O'Mara
89d7e94f77 Increment version 2020-04-12 17:23:31 +10:00
Ciarán O'Mara
aec919c713 Use unsafe copy 2020-03-21 17:34:10 +11:00
Ciarán O'Mara
6ae1180cfa Merge branch 'hotfix/header' 2020-03-21 17:28:02 +11:00
Ciarán O'Mara
429f69d84b Merge branch 'master' into develop 2020-03-21 17:28:02 +11:00
Ciarán O'Mara
d0e2560ec4 Correct header parsing 2020-03-21 17:18:39 +11:00
Ciarán O'Mara
e69c6de586 Equality comparators 2020-03-21 17:18:34 +11:00
Ciarán O'Mara
f6846edfb1 Check header in roundtrip 2020-03-21 17:16:14 +11:00
Ciarán O'Mara
cc2af1976b Use broadcast 2020-03-21 12:52:50 +11:00