millironx/XAM.jl
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Author SHA1 Message Date
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
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
6ae1180cfa Merge branch 'hotfix/header' 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
031751f6b3 Increment version 2020-03-21 00:41:24 +11:00
Ciarán O'Mara
c139754845 Merge branch 'release/v0.2.0' 2020-03-16 22:18:30 +11:00
Ciarán O'Mara
8702799593 Increment version 2020-03-16 21:59:40 +11:00
Ciarán O'Mara
2aaab4d9ab Merge branch 'feature/transcodingstreams' into develop 2020-03-16 21:56:24 +11:00
Ciarán O'Mara
de56faf066 Migrate from BufferedStreams to TranscodingStreams 2020-03-13 23:01:25 +11:00
Ciarán O'Mara
12db2c4ea8 Align emission symbols for TranscodingStreams 2020-03-13 23:01:25 +11:00
Ciarán O'Mara
6cd89aba08 Move isinteractive into machine 2020-03-13 23:01:25 +11:00
Ciarán O'Mara
892ad0d7dc Pipe into eval 2020-03-13 23:01:25 +11:00
Ciarán O'Mara
e63ce2e398 Group Automa into readrecord.jl 2020-03-13 23:01:25 +11:00
Ciarán O'Mara
365f7922fa Quick fix for BioGenerics.ReaderHelper functions 
This fix is likely to be replaced when migrating to TranscodingStreams.
 2020-03-13 23:01:25 +11:00
Ciarán O'Mara
c59a157675 Quick fix for BioCore.Ragel.State 
This fix is likely to be replaced when migrating to TranscodingStreams.
 2020-03-13 23:01:25 +11:00
Ciarán O'Mara
2cad552f63 Quick fix for BioCore.RecordHelper: unsafe_parse_decimal 2020-03-13 23:01:25 +11:00
Ciarán O'Mara
c4f3c4b0df Migrate to BioGenerics 
Basic find and replace.
 2020-03-13 23:01:25 +11:00
Ciarán O'Mara
e8ad60b086 Use accessor functions 2020-03-13 22:58:34 +11:00
Ciarán O'Mara
b0069d6f27 Preallocate 2020-03-13 22:58:34 +11:00
Ciarán O'Mara
789cccbaff Flatten elseif 2020-03-13 22:58:34 +11:00
Ciarán O'Mara
ef99c70317 Flatten returns 2020-03-13 22:58:34 +11:00
Ciarán O'Mara
7a4d6d143d Merge branch 'master' into develop 2020-03-13 22:58:02 +11:00
Ciarán O'Mara
5aca5f0011 Merge branch 'hotfix/SAM' 2020-03-13 22:42:25 +11:00
Ciarán O'Mara
f272b41031 Flatten 2020-03-13 22:09:28 +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
Konrad Herbst
8d14563f9d 🐛 Fix SAM.alignlength(record::Record)::Int (#37) 
Fixes issue #37 by re-initializing `len` in `SAM.alignlength`.
 2020-03-13 20:41:06 +11:00
Ciarán O'Mara
6f03bef623 Increment version 2020-03-13 20:41:06 +11:00
Ciarán O'Mara
406d290b13 Merge branch 'master' into develop 2020-02-28 16:18:23 +11:00
Ciarán O'Mara
109f25bd52 Merge branch 'release/v0.1.0' 2020-02-28 16:18:23 +11:00
Ciarán O'Mara
085a724b4f Update project status 2020-02-28 14:30:56 +11:00
Ciarán O'Mara
1bcd7c344c Documentation 
- API autodocs.
- Inline links for documenter.
- Logo.
- Badges.
 2020-02-28 14:29:53 +11:00
Ciarán O'Mara
30a9911e58 Documentation roundup 2020-02-28 12:27:34 +11:00
Ciarán O'Mara
bf835d9ff0 Add documentation workflow 2020-02-28 12:27:34 +11:00
Ciarán O'Mara
4b0a8a6644 Add TagBot workflow 2020-02-28 12:27:34 +11:00
Ciarán O'Mara
514e2c901d Add funding 2020-02-28 12:27:25 +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
Ciarán O'Mara
282d80a758 Continuous Integration 2020-02-20 10:19:27 +11:00
Ciarán O'Mara
b2ec340474 CompatHelper workflow 2020-02-02 20:05:05 +11:00
Ciarán O'Mara
78d2329f70 Add .github templates 2020-02-02 20:05:05 +11:00