millironx/XAM.jl
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39 commits

Author SHA1 Message Date
Ciarán O’Mara
7443237129 Adjust BGZFStreams.virtualoffset 
https://github.com/BioJulia/BGZFStreams.jl/issues/22#issuecomment-874491338
 2021-07-06 18:05:49 +10:00
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
Diego Alvarez
639b8238c7 Correct scope 2020-07-08 11:57:31 +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
81dbf41798 Merge branch 'master' into develop 2020-05-22 13:03:58 +10:00
Ciarán O'Mara
8b7a2ecc2b Correct not found check 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
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
af675a2371 Merge branch 'master' into develop 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
aec919c713 Use unsafe copy 2020-03-21 17:34:10 +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
cc2af1976b Use broadcast 2020-03-21 12:52:50 +11:00
Ciarán O'Mara
08e253c297 Use collect 2020-03-21 12:52:45 +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
f272b41031 Flatten 2020-03-13 22:09:28 +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
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
07c0f925e6 Generated files 2020-01-17 16:34:47 +11:00