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Merge branch 'master' of github.com:ksumngs/HapLink.jl
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@MillironX
MillironX committed Apr 28, 2022
2 parents 6e497e2 + 16890a2 commit de41d92
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -27,3 +27,4 @@ Manifest.toml
# Files generated during compilation/testing
build
example/output.*
example/reference.fasta.fai
5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,11 @@ Versioning](https://semver.org/spec/v2.0.0.html).
- `haplink consensus` command to generate consensus sequences from variant calls
([#29](https://github.com/ksumngs/HapLink.jl/pull/29))

### Changed

- `haplink haplotypes` now calls haplotypes based on the consensus sequence
([#30](https://github.com/ksumngs/HapLink.jl/pull/30))

## [0.6.1] - 2022-03-28

### Fixed
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4 changes: 2 additions & 2 deletions example/reference.fasta
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@@ -1,2 +1,2 @@
>MH258848.1
AGAAGTTTATCTGTGTGAACTTCTTGGCTTAGTATCGTTGAGAAGAATCGAGAGATTAGTGCAGTTTAAACAGTTTTTTAGAACGGAAGATAACCATGACTAAAAAACCAGGAGGGCCCGGTAAAAACCGGGCTATCAATATGCTGAAACGCGGCCTACCCCGCGTATTCCCACTAGTGGGAGTGAAGAGGGTAGTAATGAGCTTGTTGGACGGCAGAGGGCCAGTACGTTTCGTGCTGGCTCTTATCACGTTCTTCAAGTTTACAGCATTAGCCCCGACCAAGGCGCTTTTAGGCCGATGGAAAGCAGTGGAAAAGAGTGTGGCAATGAAACATCTTACTAGTTTCAAACGAGAACTTGGAACACTCATTGACGCCGTGAACAAGCGGGGCAGAAAGCAAAACAAAAGAGGAGGAAATGAAGGCTCAATCATGTGGCTCGCGAGCTTGGCAGTTGTCATAGCTTGTGCAGGAGCCATGAAGTTGTCGAATTTCCAGGGGAAGCTTTTGATGACCATCAACAACACGGACATTGCAGACGTTATCGTGATTCCCACCTCAAAAGGAGAGAACAGATGCTGGGTCCGGGCAATCGACGTCGGCTACATGTGTGAGGACACTATCACGTACGAATGTCCTAAGCTTACCATGGGCAATGATCCAGAGGATGTGGATTGCTGGTGTGACAACCAAGAAGTCTACGTCCAATATGGACGGTGCACGCGGACCAGGCATTCCAAGCGAAGCAGGAGATCCGTGTCGGTCCAAACACATGGGGAGAGTTCACTAGTGAATAAAAAAGAGGCTTGGCTGGATTCAACGAAAGCCACACGATATCTCATGAAAACTGAGAACTGGATCATAAGGAATCCTGGCTATGCTTTCCTGGCGGCGGTACTTGGCTGGATGCTTGGCAGTAACAACGGTCAACGCGTGGTATTTACCATCCTCCTGCTGTTGGTCGCTCCGGCTTACAGTTTTAATTGTCTGGGAATGGGCAATCGTGACTTCATAGAAGGAGCCAGTGGAGCCACTTGGGTGGACTTGGTGCTAGAAGGAGATAGCTGCTTGACAATCATGGCAAACGACAAACCAACATTGGACGTCCGCATGATTAACATCGAAGCTAGCCAACTTGCTGAGGTCAGAAGTTACTGCTATCATGCTTCAGTCACTGACATCTCGACGGTGGCTCGGTGCCCCACGACTGGAGAAGCCCACAACGAGAAGCGAGCTGATAGTAGCTATGTGTGCAAACAAGGCTTCACTGACCGTGGGTGGGGCAACGGATGTGGACTTTTCGGGAAGGGAAGCATTGACACATGTGCAAAATTCTCCTGCACCAGTAAAGCGATTGGGAGAACAATCCAGCCAGAAAACATCAAATACGAAGTTGGCATTTTTGTGCATGGAACCACCACTTCGGAAAACCATGGGAATTATTCAGCGCAAGTTGGGGCGTCCCAGGCGGCAAAGTTTACAGTAACACCCAATGCTCCTTCGATAACCCTCAAACTTGGTGACTACGGAGAAGTCACACTGGACTGTGAGCCAAGGAGTGGACTGAACACTGAAGCGTTTTACGTCATGACCGTGGGGTCAAAGTCATTTCTGGTCCATAGGGAGTGGTTTCATGACCTCGCTCTCCCCTGGACGTCCCCTTCGAGCACAGCGTGGAGAAACAGAGAACTCCTCATGGAATTTGAAGGGGCGCACGCCACAAAACAGTCCGTTGTTGCTCTTGGGTCACAGGAAGGAGGCCTCCATCAGGCGTTGGCAGGAGCCATCGTGGTGGAGTACTCAAGCTCAGTGAAGTTAACATCAGGCCACCTGAAATGTAGGCTGAAAATGGACAAACTGGCTCTGAAAGGCACAACCTATGGCATGTGTACAGAAAAATTCTCGTTCGCGAAAAATCCGGCGGACACTGGTCACGGAACAGTTGTCATTGAACTCTCCTACTCTGGGAGTGATGGCCCCTGCAAAATTCCGATTGTTTCCGTTGCGAGCCTCAATGACATGACCCCCGTTGGGCGGCTGGTGACAGTGAACCCCTTCGTCGCGACTTCCAGTGCCAACTCAAAGGTGCTGGTCGAGATGGAACCCCCCTTCGGAGACTCCTACATCGTAGTTGGAAGGGGAGACAAGCAGATCAACCACCATTGGCACAAAGCTGGAAGCACGCTGGGCAAGGCCTTTTCAACAACTTTGAAGGGAGCTCAAAGACTGGCAGCGTTGGGCGACACAGCCTGGGACTTTGGCTCTATTGGAGGGGTCTTCAACTCCATAGGAAAAGCCGTTCACCAAGTGTTTGGTGGTGCCTTCAGAACACTCTTTGGGGGAATGTCTTGGATCACACAAGGGCTAATGGGTGCCCTACTGCTCTGGATGGGCGTCAACGCACGAGACCGATCAATTGCTTTGGCCTTCTTAGCCACAGGGGGTGTGCTCGTGTTCTTAGCGACCAATGTGCATGCTGACACTGGATGTGCCATTGACATCACAAGAAAAGAGATGAGATGTGGAAGTGGCATCTTCGTGCACAACGACGTGGAAGCCTGGGTGGATAGGTATAAATATTTGCCAGAAACGCCCAGATCCCTAGCGAAGATCGTCCACAAAGCGCACAAGGAAGGCGTGTGCGGAGTCAGATCTGTCACTAGACTGGAGCACCAAATGTGGGAAGCCGTACGGGACGAATTGAACGTCCTGCTCAAAGAGAATGCAGTGGACCTCAGTGTGGTTGTGAACAAGCCCGTGGGAAGATATCGCTCAGCCCCTAAACGCCTATCCATGACGCAAGAGAAGTTTGAAATGGGCTGGAAAGCATGGGGAAAAAGCATTCTCTTTGCCCCGGAATTGGCTAACTCCACATTTGTCGTAGATGGACCTGAGACAAAGGAATGCCCTGATGAGCACAGAGCTTGGAACAGCATGCAAATCGAAGACTTCGGCTTTGGCATCACATCAACCCGTGTGTGGCTGAAAATTAGAGAGGAGAGCACTGACGAGTGTGATGGAGCGATCATAGGCACGGCTGTCAAAGGACATGTGGCAGTCCATAGTGACTTGTCGTACTGGATTGAGAGTCGCTACAACGACACATGGAAACTTGAGAGGGCAGTCTTTGGAGAGGTCAAATCTTGCACTTGGCCAGAGACACACACCCTTTGGGGAGATGATGTTGAGGAAAGTGAACTCATCATTCCGCACACCATAGCCGGACCAAAAAGCAAGCACAATCGGAGGGAAGGGTATAAGACACAAAACCAGGGACCTTGGGATGAGAATGGCATAGTCTTGGACTTTGATTATTGCCCAGGGACAAAAGTCACCATTACAGAGGATTGTGGCAAGAGAGGCCCTTCGGTCAGAACCACTACTGACAGTGGAAAGTTGATCACTGACTGGTGCTGTCGCAGTTGCTCCCTTCCGCCCCTACGATTCCGGACAGAAAATGGCTGCTGGTACGGAATGGAAATCAGACCTGTTAGGCATGATGAAACAACACTCGTCAGATCACAGGTTGATGCTTTCAATGGTGAAATGGTTGACCCTTTTCAGCTGGGCCTTCTGGTGATGTTTCTGGCCACCCAGGAGGTCCTTCGCAAGAGGTGGACGGCCAGATTGACCATTCCTGCGGTTTTGGGGGCCCTACTTGTGCTGATGCTTGGGGGCATCACTTACACTGATTTGGCGAGGTATGTGGTGCTAGTCGCTGCTGCTTTCGCAGAGGCCAACAGTGGAGGAGACGTCCTGCACCTTGCTTTGATTGCCGTTTTTAAGATCCAACCAGCATTTCTAGTGATGAACATGCTTAGCACGAGATGGACGAACCAAGAAAACGTGGTTCTGGTCCTAGGGGCTGCCTTTTTCCAATTGGCCTCAGTAGATCTGCAAATAGGAGTCCACGGAATCCTGAATGCCGCCGCTATAGCATGGATGATTGTCCGAGCGATCACCTTCCCCACAACCTCCTCCGTCACCATGCCAGTCTTAGCGCTTCTAACTCCGGGGATGAGGGCTCTATACCTAGACACTTACAGAATCATCCTCCTCGTCATAGGGATTTGCTCCCTGCTGCACGAGAGGAAAAAGACCATGGCAAAAAAGAAAGGAGCTGTACTCTTGGGCTTAGCGCTCACATCCACTGGATGGTTCTCGCCCACCACTATAGCTGCCGGACTAATGGTCTGCAACCCAAACAAGAAGAGAGGGTGGCCAGCTACTGAGTTTTTGTCGGCAGTTGGATTGATGTTTGCCATCGTAGGTGGTTTGGCCGAGTTGGATATTGAATCCATGTCAATACCCTTCATGCTGGCAGGTCTCATGGCAGTGTCCTACGTGGTGTCAGGAAAAGCAACAGATATGTGGCTTGAACGGGCCGCCGACATCAGCTGGGAGATGGATGCTGCAATCACAGGAAGCAGTCGGAGGCTGGATGTGAAACTGGATGATGACGGAGATTTTCACTTGATTGATGATCCCGGTGTTCCATGGAAGGTCTGGGTCCTGCGCATGTCTTGCATTGGCTTAGCCGCCCTCACGCCTTGGGCCATCGTTCCCGCCGCTTTCGGTTATTGGCTCACTTTAAAAACAACAAAAAGAGGGGGCGTGTTTTGGGACACGCCATCCCCAAAACCTTGCTCAAAAGGAGACACCACTACAGGAGTCTACCGAATTATGGCTAGAGGGATTCTTGGCACTTACCAGGCCGGCGTCGGAGTCATGTACGAGAATGTTTTCCACACACTATGGCACACAACTAGAGGAGCAGCCATTATGAGTGGAGAAGGAAAATTGACGCCATACTGGGGTAGTGTGAGAGAAGACCGCATAGCTTACGGAGGCCCATGGAGGTTTGACCGAAAATGGAATGGAACAGATGACGTGCAAGTGATCGTGGTAGAACCGGGGAAGGCTGCAGTAAACATCCAGACAAAACCAGGAGTGTTTCGGACTCCCTTCGGGGAGGTTGGGGCTGTTAGTCTGGATTACCCGCGAGGAACATCCGGCTCACCCATTCTGGATTCCAATGGAGACATTATAGGCCTATACGGCAATGGAGTTGAGCTTGGCGATGGCTCATACGTCAGCGCCATCGTGCAGGGTGACCGTCAGGAGGAACCAGTCCCAGAAGCTTACACCCCAAACATGTTGAGAAAGAGACAGATGACTGTGCTAGATTTGCACCCTGGTTCAGGGAAAACCAGGAAAATTCTGCCACAAATAATTAAGGACGCTATCCAGCAGCGCCTAAGAACAGCTGTGTTGGCACCGACGCGGGTGGTAGCAGCAGAAATGGCAGAAGCTTTGAGAGGGCTCCCAGTACGATATCAAACTTCAGCAGTGCAGAGAGAGCACCAAGGGAATGAAATAGTGGATGTGATGTGCCACGCCACTCTGACCCATAGACTGATGTCACCGAACAGAGTGCCCAACTACAACCTATTTGTCATGGATGAAGCTCATTTCACCGACCCAGCCAGTATAGCCGCACGAGGATACATTGCTACCAAGGTGGAATTAGGGGAGGCAGCAGCCATCTTTATGACAGCGACCCCGCCTGGAACCACGGATCCTTTTCCTGACTCAAATGCCCCAATCCATGATTTGCAAGATGAGATACCAGACAGGGCATGGAGCAGTGGATACGAATGGATCACAGAATATGCGGGTAAAACCGTGTGGTTTGTGGCGAGCGTAAAAATGGGGAATGAGATTGCAATGTGCCTCCAAAGAGCGGGGAAAAAGGTCATCCAACTCAACCGCAAGTCCTATGACACAGAATACCCAAAATGTAAGAATGGAGACTGGGATTTTGTCATTACCACCGACATCTCTGAAATGGGGGCCAACTTCGGTGCGAGCAGGGTCATCGACTGTAGAAAGAGCGTGAAACCCACCATCTTAGAAGAGGGAGAAGGCAGAGTCATCCTCGGAAACCCATCTCCCATAACCAGTGCAAGCGCAGCTCAACGGAGGGGCAGAGTAGGCAGAAACCCCAACCAAGTTGGAGATGAATACCACTATGGGGGGGCTACCAGTGAAGATGACAGTAACCTAGCCCATTGGACAGAGGCAAAGATCATGTTAGACAACATACACATGCCCAATGGACTGGTGGCCCAGCTCTATGGACCAGAGAGGGAAAAGGCTTTCACAATGGATGGCGAATACCGTCTCAGAGGTGAAGAAAAGAAAAACTTCTTAGAGCTGCTTAGGACGGCTGACCTCCCGGTGTGGCTGGCCTACAAGGTGGCGTCCAATGGCATTCAGTACACCGACAGAAAGTGGTGTTTTGATGGGCCGCGTACGAATGCCATACTGGAGGACAACACCGAGGTAGAGATAGTCACCCGGATGGGTGAGAGGAAAATCCTCAAGCCGAGATGGCTTGATGCAAGAGTTTATGCAGATCACCAAGCCCTCAAGTGGTTCAAAGACTTTGCAGCAGGGAAGAGATCAGCCGTTAGCTTCATAGAGGTGCTCGGTCGCATGCCTGAGCATTTCATGGGAAAGACGCGGGAAGCTTTAGACACCATGTACTTGGTTGCAACGGCTGAGAAAGGTGGGAAAGCACACCGAATGGCTCTCGAAGAGCTGCCAGATGCACTGGAAACCATCACACTTATTGTCGCCATTACTGTGATGACAGGAGGATTCTTCCTACTAATGATGCAGCGAAAGGGTATAGGGAAGATGGGTCTTGGAGCTCTAGTGCTCACGCTAGCTACCTTCTTCCTGTGGGCGGCAGAGGTTCCTGGAACCAAAATAGCAGGGACCCTGCTGATCGCCCTGCTGCTGATGGTGGTTCTCATCCCAGAACCGGAAAAACAGAGGTCACAGACAGATAACCAACTGGCGGTGTTTCTCATCTGTGTCTTGACCGTGGTTGGAGTGGTGGCAGCAAACGAGTACGGGATGCTAGAAAAAACCAAAGCAGATCTCAAGAGCATGTTTGGCGGAAAGACGCAGGCATCAGGACTGACTGGATTGCCAAGCATGGCACTGGACCTGCGTCCAGCCACAGCCTGGGCACTGTATGGGGGGAGCACAGTCGTGCTAACCCCTCTTCTGAAGCACCTGATCACGTCGGAATACGTCACCACATCGCTAGCCTCAATTAACTCACAAGCTGGCTCATTATTCGTCTTGCCACGAGGCGTGCCTTTTACCGACCTAGACTTGACCGTTGGCCTCGTCTTCCTTGGCTGTTGGGGTCAAATCACCCTCACAACGTTTCTGACAGCCATGGTTCTGGCGACACTTCACTATGGGTACATGCTCCCTGGATGGCAAGCAGAAGCACTCAGGGCTGCCCAGAGAAGGACAGCGGCTGGAATAATGAAGAATGCCGTTGTTGACGGAATGGTCGCCACTGATGTGCCTGAACTGGAAAGGACTACTCCTCTGATGCAAAAGAAAGTCGGACAGGTGCTCCTCATAGGGGTAAGCGTGGCAGCGTTCCTCGTCAACCCTAATGTCACCACTGTGAGAGAAGCAGGGGTGTTGGTGACGGCGGCTACGCTTACTTTGTGGGACAATGGAGCCAGTGCCGTTTGGAATTCCACCACAGCCACGGGACTCTGCCATGTCATGCGAGGTAGCTACCTGGCTGGAGGCTCCATTGCTTGGACTCTCATCAAGAACGCTGATAAGCCCTCCTTGAAAAGGGGAAGGCCTGGGGGCAGGACGCTAGGGGAGCAGTGGAAGGAAAAACTAAATGCCATGAGCAGAGAAGAGTTTTTTAAATACCGGAGAGAGGCCATAATCGAGGTGGACCGCACTGAAGCACGCAGGGCCAGACGTGAAAATAACATAGTGGGAGGACATCCGGTTTCGCGAGGCTCAGCAAAACTCCGTTGGCTCGTGGAGAAAGGATTTGTCTCGCCAATAGGAAAAGTCATTGATCTAGGGTGTGGGCGTGGAGGATGGAGCTACTACGCAGCAACCCTGAAGAAGGTCCAGGAAGTCAGAGGATACACGAAAGGTGGGGCGGGACATGAAGAACCGATGCTCATGCAGAGCTACGGCTGGAACCTGGTCTCCCTGAAGAGTGGAGTGGACGTGTTTTACAAACCTTCAGAGCCCAGTGACACCCTGTTCTGTGACATAGGGGAATCCTCCCCAAGTCCAGAAGTAGAAGAACAACGCACACTACGCGTCCTAGAGATGACATCTGACTGGTTGCACCGAGGACCTAGAGAGTTCTGCATTAAAGTTCTCTGCCCTTACATGCCCAAGGTTATAGAAAAAATGGAAGTTCTGCAGCGCCGCTTCGGAGGTGGGCTAGTGCGTCTCCCCCTGTCCCGAAACTCCAATCACGAGATGTATTGGGTTAGTGGAGCCGCTGGCAATGTGGTGCACGCTGTGAACATGACCAGCCAGGTACTACTGGGGCGAATGGATCGCACAGTGTGGAGAGGGCCAAAGTATGAGGAAGATGTCAACCTAGGGAGCGGAACAAGAGCCGTGGGAAAGGGAGAAGTCCATAGCAATCAGGAGAAAATCAAGAAGAGAATCCAGAAGCTTAAAGAAGAATTCGCCACAACGTGGCACAAAGACCCTGAGCATCCATACCGCACTTGGACATACCACGGAAGCTATGAAGTGAAGGCTACTGGCTCAGCCAGCTCTCTCGTCAACGGAGTGGTGAAGCTCATGAGCAAACCTTGGGACGCCATTGCCAACGTCACCACCATGGCCATGACTGACACCACCCCTTTTGGACAGCAAAGAGTTTTCAAGGAGAAAGTTGACACGAAGGCTCCTGAGCCACCAGCTGGAGCCAAGGAAGTGCTCAACGAGACCACCAACTGGCTGTGGGCCCACTTGTCACGGGAAAAAAGACCCCGCTTGTGCACCAAGGAAGAATTCATAAAGAAAGTCAACAGCAACGCGGCTCTTGGAGCAGTGTTCGCTGAACAGAATCAATGGAGCACGGCGCGTGAGGCTGTGGATGACCCGCGGTTTTGGGAGATGGTTGATGAAGAGAGGGAAAACCATCTGCGAGGAGAGTGTCACACATGTATCTACAACATGATGGGAAAAAGAGAGAAGAAGCCTGGAGAGTTTGGAAAAGCTAAAGGAAGCAGGGCCATTTGGTTCATGTGGCTTGGAGCACGGTATCTAGAGTTTGAAGCTTTGGGGTTCCTGAATGAAGACCATTGGCTGAGCCGAGAGAATTCAGGAGGTGGAGTGGAAGGCTCAGGCGTCCAAAAGCTGGGATACATCCTCCGTGACATAGCAGGAAAGCAAGGAGGGAAAATGTACGCTGATGATACCGCCGGGTGGGACACTAGAATTACCAGAACTGATTTAGAAAATGAAGCTAAGGTACTGGAGCTCCTAGACGGTGAACACCGCATGCTCGCCCGAGCCATAATTGAACTGACTTACAGGCACAAAGTGGTCAAGGTCATGAGACCTGCAGCAGAAGGAAAGACCGTGATGGACGTGATATCAAGAGAAGATCAAAGGGGGAGTGGACAGGTGGTCACTTATGCTCTTAACACTTTCACGAACATCGCTGTCCAGCTCGTCAGGCTGATGGAGGCTGAGGGGGTCATTGGACCACAACACTTGGAACAGCTACCTAGGAAAAACAAGATAGCTGTCAGGACCTGGCTCTTTGAGAATGGAGAGGAGAGAGTGACCAGGATGGCGATCAGCGGAGACGACTGTGTCGTCAAGCCGCTGGACGACAGATTCGCCACAGCCCTCCACTTCCTCAACGCAATGTCAAAGGTCAGAAAAGACATCCAGGAATGGAAGCCTTCGCATGGCTGGCACGATTGGCAGCAAGTTCCCTTCTGCTCTAACCATTTTCAGGAGATTGTGATGAAAGATGGAAGGAGTATAGTTGTCCCGTGCAGAGGACAGGATGAGCTGATAGGCAGGGCTCGCATCTCTCCAGGAGCTGGATGGAATGTGAAGGACACAGCTTGCCTGGCCAAAGCATATGCACAGATGTGGCTACTCCTATACTTCCATCGCAGGGACTTGCGTCTCATGGCAAATGCGATTTGCTCAGCAGTGCCAGTGGATTGGGTGCCCACAGGCAGGACATCCTGGTCAATACACTCGAAAGGAGAGTGGATGACCACGGAAGACATGCTGCAGGTCTGGAACAGAGTCTGGATTGAAGAAAATGAATGGATGATGGACAAGACTCCAATCACAAGCTGGACAGACGTTCCGTATGTGGGAAAGCGTGAGGACATCTGGTGTGGCAGCCTCATCGGAACGCGATCCAGAGCAACCTGGGCTGAGAACATCTATGCGGCGATAAACCAGGTTAGAGCTGTCATTGGGAAAGAAAATTATGTTGACTACATGACCTCACTCAGGAGATACGAAGACGTCTTGATCCAGGAAGACAGGGTCATCTAGTGTGATTTAAGGTAGAAAAGTAGACTATGTAAATAATGTAAATGAGAAAATGCATGCATATGGAGTCAGGCCAGCAAAAGCTGCCACCGGATACTGGGTAGACGGTGCTGCCTGCGTCTCAGTCCCAGGAGGACTGGGTTAACAAATCTGACAACAGAAAGTGAGAAAGCCCTCAGAACCGTCTCGGAAGTAGGTCCCTGCTCACTGGAAGTTGAAAGACCAACGTCAGGCCACAAATTTGTGCCACTCCGCTAGGGAGTGCGGCCTGCGCAGCCCCAGGAGGACTGGGTTACCAAAGCCGTTGAGGCCCCCACGGCCCAAGCCTCGTCTAGGATGCAATAGACGAGGTGTAAGGACTAGAGGTTAGAGGAGACCCCGTGGAAACAACAACATGCGGCCCAAGCCCCCTCGAAGCTGTAGAGGAGGTGGAAGGACTAGAGGTTAGAGGAGACCCCGCATTTGCATCAAACAGCATATTGACACCTGGGAATAGACTGGGAGATCTTCTGCTCTATCTCAACATCAGCTACTAGGCACAGAGCGCCGAAGTATGTAGCTGGTGGTGAGGAAGAACACAGGATCT
>reference
ACAACTTTATCTCTCTCAACTTCTTCCCTTACTATCCTTCACAACAATCCACACATTACTGCACTTTAAACACTTTTTTA
1 change: 0 additions & 1 deletion example/reference.fasta.fai
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211 changes: 167 additions & 44 deletions example/sample.yaml
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Original file line number Diff line number Diff line change
@@ -1,61 +1,184 @@
version: "0.6.1"
settings:
variants: "example/output.vcf"
method: "ml-template"
output: "example/output.yaml"
depth: 1
overlap_max: 100
bam: "example/sample.bam"
overlap_min: 0
iterations: 1000
reference: "example/reference.fasta"
significance: 0.5
seed: ~
haplotypes:
- name: cda90415
frequency: 0.4
- name: "CONSENSUS"
linkage: 1.0
frequency: 0.6
significance: 0.0
snps:
- chromosome: MH258848.1
position: 1115
referencebase: T
alternatebase: C
identifier: .
quality: 30
- chromosome: "reference"
position: 17
identifier: "."
referencebase: C
alternatebase: G
quality: 30.0
filter: PASS
info:
- chromosome: MH258848.1
position: 3110
referencebase: A
DP: 3
AD: 3
- chromosome: "reference"
position: 26
identifier: "."
referencebase: C
alternatebase: G
identifier: .
quality: 30
quality: 30.0
filter: PASS
info:
- chromosome: MH258848.1
position: 6948
DP: 5
AD: 5
- chromosome: "reference"
position: 27
identifier: "."
referencebase: C
alternatebase: A
identifier: .
quality: 30
alternatebase: G
quality: 30.0
filter: PASS
info:
- name: 063ccada
frequency: 0.3
snps:
- chromosome: MH258849.1
position: 8714
DP: 5
AD: 5
- chromosome: "reference"
position: 29
identifier: "."
referencebase: T
alternatebase: C
identifier: .
quality: 30
alternatebase: A
quality: 63.0
filter: PASS
info:
- chromosome: MH258849.1
position: 4931
DP: 5
AD: 3
- chromosome: "reference"
position: 32
identifier: "."
referencebase: C
alternatebase: T
identifier: .
quality: 30
alternatebase: G
quality: 30.0
filter: PASS
info:
- name: ebde7a35
frequency: 0.2
snps:
- chromosome: MH258848.1
position: 7172
referencebase: T
alternatebase: C
identifier: .
quality: 30
filter: PASS
info:
- name: 75cec553
frequency: 0.1
DP: 6
AD: 6
- chromosome: "reference"
position: 37
identifier: "."
referencebase: C
alternatebase: G
quality: 30.0
filter: PASS
info:
DP: 6
AD: 6
- chromosome: "reference"
position: 40
identifier: "."
referencebase: C
alternatebase: G
quality: 30.0
filter: PASS
info:
DP: 6
AD: 6
- chromosome: "reference"
position: 42
identifier: "."
referencebase: C
alternatebase: G
quality: 30.0
filter: PASS
info:
DP: 6
AD: 6
- chromosome: "reference"
position: 45
identifier: "."
referencebase: C
alternatebase: G
quality: 30.0
filter: PASS
info:
DP: 6
AD: 6
- chromosome: "reference"
position: 50
identifier: "."
referencebase: C
alternatebase: G
quality: 30.0
filter: PASS
info:
DP: 6
AD: 6
- chromosome: "reference"
position: 52
identifier: "."
referencebase: C
alternatebase: G
quality: 30.0
filter: PASS
info:
DP: 6
AD: 6
- chromosome: "reference"
position: 54
identifier: "."
referencebase: C
alternatebase: G
quality: 30.0
filter: PASS
info:
DP: 6
AD: 6
- chromosome: "reference"
position: 59
identifier: "."
referencebase: C
alternatebase: G
quality: 30.0
filter: PASS
info:
DP: 5
AD: 5
- chromosome: "reference"
position: 64
identifier: "."
referencebase: C
alternatebase: G
quality: 30.0
filter: PASS
info:
DP: 3
AD: 3
- name: "e76e867c"
linkage: 0.0
frequency: 1.0
significance: .NaN
snps:
- chromosome: "reference"
position: 34
identifier: "."
referencebase: A
alternatebase: T
quality: 20.0
filter: PASS
info:
DP: 6
AD: 3
- chromosome: "reference"
position: 48
identifier: "."
referencebase: T
alternatebase: A
quality: 63.0
filter: PASS
info:
DP: 6
AD: 3
12 changes: 10 additions & 2 deletions precompile_app.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,14 @@ push!(ARGS, "--output")
push!(ARGS, "example/output.vcf")
push!(ARGS, "--quality")
push!(ARGS, "12")
push!(ARGS, "--frequency")
push!(ARGS, "0.001")
push!(ARGS, "--position")
push!(ARGS, "0.001")
push!(ARGS, "--significance")
push!(ARGS, "0.5")
push!(ARGS, "--depth")
push!(ARGS, "1")

HapLink.haplink()
clear_args()
Expand Down Expand Up @@ -42,9 +50,9 @@ push!(ARGS, "example/reference.fasta")
push!(ARGS, "--output")
push!(ARGS, "example/output.yaml")
push!(ARGS, "--significance")
push!(ARGS, "0.05")
push!(ARGS, "0.5")
push!(ARGS, "--depth")
push!(ARGS, "50")
push!(ARGS, "1")
push!(ARGS, "--method")
push!(ARGS, "raw")

Expand Down
21 changes: 17 additions & 4 deletions src/HapLink.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,10 @@ using SHA
using XAM
using YAML

export consensus
export chromosome
export consensus_sequence
export consensus_variants
export frequency
export read_vcf

const VERSION = ArgParse.project_version(
Expand Down Expand Up @@ -327,7 +330,7 @@ function _consensus(arguments::Dict{String,Any})

refseq = FASTA.sequence(_first_record(reffile))

conseq = consensus(refseq, variants; freq=frequency)
conseq = consensus_sequence(refseq, variants; freq=frequency)

FASTA.Writer(open(outfile, "w")) do f
write(f, FASTA.Record("$(prefix)_CONSENSUS", conseq))
Expand Down Expand Up @@ -395,11 +398,21 @@ function sequences(arguments::Dict{String,Any})
ffile = arguments["output"]

haplodata = YAML.load_file(hfile)["haplotypes"]
haplotypes = Haplotype.(map(f -> Variant.(f["snps"]), haplodata))
consensus_snps = first(filter(d -> d["name"] == "CONSENSUS", haplodata))["snps"]
consensus_hap = Haplotype(Variant.(consensus_snps))

otherhaps = filter(d -> d["name"] != "CONSENSUS", haplodata)
haplotypes = Haplotype.(map(f -> Variant.(f["snps"]), otherhaps))

refrec = _first_record(rfile)

newrecords = unique(mutate.([refrec], haplotypes))
conrec = FASTA.Record(
FASTA.identifier(refrec),
FASTA.description(refrec),
mutate(FASTA.sequence(refrec), consensus_hap),
)

newrecords = unique(mutate.([conrec], haplotypes))

open(FASTA.Writer, ffile) do f
for r in newrecords
Expand Down
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