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Create basic SequenceDistanceGraph and DBG building based on Arda's code #10

Merged
merged 14 commits into from
Jul 9, 2019
Merged

Create basic SequenceDistanceGraph and DBG building based on Arda's code #10

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f53160b
Create basic SequenceDistanceGraph and DBG building based on Arda's code
Jul 2, 2019
bc1b291
Fix some minor typos
Jul 3, 2019
bebf19f
Remove unused find_overlaps method from SequenceDistanceGraph
Jul 3, 2019
27ac3ee
New unitig graph builder
Jul 6, 2019
92d3f8f
Fix CI files
Jul 6, 2019
d083a54
Move some functions
Jul 6, 2019
9f85cae
Add a check for unused kmers at the end of unitig creation.
Jul 6, 2019
3460065
Add a dump to GFA1 method
Jul 6, 2019
f74cfe4
Add debug messages to the unitig builder and make it distinct function
Jul 8, 2019
eb4bea0
Edit debugging messages
Jul 8, 2019
adea581
Extract unitig overlap finding to its own function
Jul 8, 2019
97ccb24
Update travis
Jul 8, 2019
1237a4d
Update unitig graph builder
Jul 8, 2019
c434dc8
Move files
Jul 9, 2019
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -3,3 +3,5 @@
*.jl.mem
*.jld
.DS_Store
Manifest.toml
.ipynb_checkpoints
7 changes: 3 additions & 4 deletions .travis.yml
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Expand Up @@ -4,12 +4,11 @@ os:
- linux
- osx
julia:
- 0.6
- 1.1
- 1.2
- nightly
notifications:
email: false
git:
depth: 99999999
email: benjward@protonmail.com

## uncomment the following lines to allow failures on nightly julia
## (tests will run but not make your overall status red)
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302 changes: 0 additions & 302 deletions Manifest.toml
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14 changes: 10 additions & 4 deletions Project.toml
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Expand Up @@ -6,7 +6,13 @@ version = "0.1.0"
[deps]
Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
JLD = "4138dd39-2aa7-5051-a626-17a0bb65d9c8"
Pseudoseq = "5fa9f68e-f4b0-11e8-18b8-fb82dd3c6483"
TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"

[compat]
BioSequences = "1.1"
julia = "1.1"

[extras]
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["Test"]
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