Merge pull request #2 from nvnieuwk/dev

Version 0.1.0

.github/workflows/go.yml

@@ -0,0 +1,31 @@
+# This workflow will build a golang project
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-go
+
+name: Go
+
+on:
+  push:
+    branches: [ "main", "dev" ]
+  pull_request:
+    branches: [ "main", "dev" ]
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Go
+      uses: actions/setup-go@v4
+      with:
+        go-version: '1.21'
+
+    - name: Install dependencies
+      run: go get .
+
+    - name: Build
+      run: go build -v ./...
+
+    - name: Test
+      run: go test -v ./...

.github/workflows/release.yml

@@ -0,0 +1,27 @@
+on:
+  release:
+    types: [created]
+
+permissions:
+    contents: write
+    packages: write
+
+jobs:
+  release-bedgovcf:
+    name: release bedgovcf ${{ matrix.goos }}_${{ matrix.goarch }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        goos: [linux, darwin]
+        goarch: [amd64, arm64]
+        exclude:
+          - goos: linux
+            goarch: arm64
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: wangyoucao577/go-release-action@v1
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        goos: ${{ matrix.goos }}
+        goarch: ${{ matrix.goarch }}

.gitignore

@@ -7,6 +7,7 @@
 *.dll
 *.so
 *.dylib
+svync
 
 # Test binary, built with `go test -c`
 *.test
@@ -19,3 +20,6 @@
 
 # Go workspace file
 go.work
+
+# Output files
+test.vcf

README.md

@@ -1,2 +1,61 @@
 # svync
-⚠️ This tool is still under development, please check back in the future ⚠️
+Svync is a tool designed to synchronize structural variant calls from different callers. It uses YAML configs to define how to handle the standardization. 
+
+## Usage
+```bash
+svync --config <config.yaml> --input <input.vcf>
+```
+
+### Arguments
+#### Required
+| Argument | Description |
+| --- | --- |
+| `--config`/`-c` | Path to the YAML config file |
+| `--input`/`-i` | Path to the input VCF file |
+
+#### Optional
+| Argument | Description | Default |
+| --- | --- | --- |
+| `--output`/`-o` | Path to the output VCF file | `stdout` |
+| `--nodate`/`--nd` | Do not add the date to the output VCF file | `false` |
+| `--mute-warnings`/`--mw` | Do not output warnings | `false` |
+
+## Configuration
+The configuration file is the core of the standardization in Svync. More information can be found in the [configuration documentation](docs/configuration.md).
+
+
+## Installation
+### Mamba/Conda
+This is the preffered way of installing BedGoVcf.
+
+```bash
+mamba install -c bioconda bedgovcf
+```
+
+or with conda:
+
+```bash 
+conda install -c bioconda bedgovcf
+```
+
+### Precompiled binaries
+Precompiled binaries are available for Linux and macOS on the [releases page](https://github.com/nvnieuwk/svync/releases).
+
+
+### Installation from source
+Make sure you have go installed on your machine (or [install](https://go.dev/doc/install) it if you don't currently have it)
+
+Then run these commands to install bedgovcf:
+
+```bash
+go get .
+go build .
+sudo mv bedgovcf /usr/local/bin/
+```
+
+Next run this command to check if it was correctly installed:
+
+```bash
+bedgovcf --help
+```
+

data/delly.yaml

@@ -0,0 +1,29 @@
+# Test config for Delly SV caller
+id: "delly_$INFO/SVTYPE"
+alt:
+  BND: TRA
+info:
+  CALLER:
+    value: delly
+    description: SV caller
+    number: 1
+    type: string
+  TEST:
+    value: $INFO/END,$INFO/CIEND/1
+    description: Test info field
+    number: 2
+    type: integer
+  SVLEN:
+    value: ~sub:$INFO/END,$POS
+    description: SV length
+    number: 2
+    type: integer
+    alts:
+      DEL: -~sub:$INFO/END,$POS
+      INS: $INFO/INSLEN
+format:
+  PE:
+    value: $FORMAT/DR,$FORMAT/DV
+    description: Paired-read support for the ref and alt alleles in the order listed
+    number: 2
+    type: integer

data/gridss.yaml

@@ -0,0 +1,36 @@
+# Test config for Delly SV caller
+id: "gridss_$INFO/SVTYPE"
+info:
+  CALLER:
+    value: gridss
+    description: SV caller
+    number: 1
+    type: string
+  CIPOS:
+    value: $INFO/CIPOS
+    description: Confidence interval around POS for imprecise variants
+    number: 2
+    type: Integer
+    alts:
+      BND:
+  CIEND:
+    value: $INFO/CIRPOS
+    description: Confidence interval around END position for imprecise variants
+    number: 2
+    type: Integer
+  SVLEN:
+    value: $INFO/SVLEN
+    description: The length of the structural variant
+    number: 1
+    type: Integer
+  IMPRECISE:
+    value: $INFO/IMPRECISE
+    description: Imprecise structural variation
+    number: 0
+    type: flag
+format:
+  GT:
+    value: ./.
+    description: Genotype
+    number: 1
+    type: string

data/test1.delly.vcf

@@ -0,0 +1,50 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20231204
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=BND,Description="Translocation">
+##ALT=<ID=INS,Description="Insertion">
+##FILTER=<ID=LowQual,Description="Poor quality and insufficient number of PEs and SRs.">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS">
+##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for POS2 coordinate in case of an inter-chromosomal translocation">
+##INFO=<ID=POS2,Number=1,Type=Integer,Description="Genomic position for CHR2 in case of an inter-chromosomal translocation">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
+##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant">
+##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
+##INFO=<ID=SRMAPQ,Number=1,Type=Integer,Description="Median mapping quality of split-reads">
+##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support">
+##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality">
+##INFO=<ID=SVINSSEQ,Number=1,Type=String,Description="Split-read consensus sequence">
+##INFO=<ID=CE,Number=1,Type=Float,Description="Consensus sequence entropy">
+##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Insertion length for SVTYPE=INS.">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
+##INFO=<ID=INSLEN,Number=1,Type=Integer,Description="Predicted length of the insertion">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Predicted microhomology length using a max. edit distance of 2">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">
+##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the SV">
+##FORMAT=<ID=RCL,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the left control region">
+##FORMAT=<ID=RCR,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the right control region">
+##FORMAT=<ID=RDCN,Number=1,Type=Integer,Description="Read-depth based copy-number estimate for autosomal sites">
+##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs">
+##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads">
+##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads">
+##reference=reference.fasta
+##contig=<ID=chr14,length=2000001>
+##contig=<ID=chr16,length=2000001>
+##contig=<ID=chrX,length=2000001>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	PosCon1
+chr16	86933	DEL00000000	T	<DEL>	120	LowQual	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.6;END=1349692;PE=0;MAPQ=0;CT=3to5;CIPOS=-9,9;CIEND=-9,9;SRMAPQ=60;INSLEN=0;HOMLEN=9;SR=2;SRQ=0.986667;SVINSSEQ=AAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAATATATATATATATATATATATATATATATATATATATACACATACATATATACGGTTGATTTTTACATATTGATCTTGTATCTTGTAACCTTGCTGAACTTGTTCATTAGTTCTAAT;CE=1.61868	GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV	1/1:-24.3989,-2.10615,0:21:PASS:0:31692:19715:3:0:0:0:7
+chr16	1077371	INV00000001	T	<INV>	58	LowQual	IMPRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv1.1.6;END=1078502;PE=2;MAPQ=29;CT=5to5;CIPOS=-392,392;CIEND=-392,392	GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV	0/0:0,-0.521621,-107.701:6:LowQual:40:102:49:2:19:2:0:0
+chr16	1123476	INV00000002	A	<INV>	180	PASS	PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv1.1.6;END=1604486;PE=0;MAPQ=0;CT=5to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=3;SRQ=0.98;SVINSSEQ=GAATTGCTTGAACACTGCACCACTGCACTCCAGCCTGGGTGACAGAGGAAGACTCTTTCTCCAAAAAAAAAGAATGTTTTCCTACATATATATATATATATATATATATATACACACACACACACACACACACACACACACACACAGTCT;CE=1.88447	GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV	1/1:-38.9839,-3.59622,0:36:PASS:11456:39951:0:7:0:0:0:12
+chr16	1135261	INS00000003	C	<INS>	299	PASS	PRECISE;SVTYPE=INS;SVMETHOD=EMBL.DELLYv1.1.6;END=1135262;SVLEN=27;PE=0;MAPQ=0;CT=NtoN;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=60;INSLEN=27;HOMLEN=2;SR=5;SRQ=1;SVINSSEQ=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCACTGGAAACAGCCAAGAGATCCTTCAAAAAGTGAATGGATAAACCAACTGTAACTCATTCATACAGTGGAACGTTAATCAGCAATTCTAAAAATGAGCTATCAAGTCACAAAAAGACAAAGAAGAACCTTAACACAAAATAACA;CE=1.67205	GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV	1/1:-90.4974,-7.52311,0:75:PASS:11619:25087:13468:2:0:0:0:25

docs/configuration.md

@@ -0,0 +1,134 @@
+# Configuration
+The configuration file consists of 4 main parts:
+1. `id` 
+2. `alt`
+3. `info`
+4. `format`
+
+## `id`
+The `id` section is used to define the ID of the variant. The `id` section can be defined as follows:
+```yaml
+id: <id>
+```
+The value for the ID can be resolved (see [Resolvable fields](#resolvable-fields)). All IDs get a unique number appended to them to ensure that they are unique.
+
+## `alt`
+The `alt` section can be used to change the ALT field and SVTYPE info field for each variant. The `alt` section can be defined as follows:
+```yaml
+alt:
+  <alt>: <new_alt>
+```
+
+For example you might want to change the `BND` ALT to `TRA` (for Delly for example):
+```yaml
+alt:
+  BND: TRA
+```
+
+## `info`
+The `info` section can be used to change the info fields for each variant. The `info` section can be defined as follows:
+```yaml
+info:
+  <info_field>:
+    value: <new_value>
+    type: <new_type>
+    description: <new_description>
+    number: <new_number>
+    alts:
+      <alt>: <new_value>
+      <alt>: <new_value>
+```
+### value
+The `value` field can be used to change the default value of the info field. The value can be resolved (see [Resolvable fields](#resolvable-fields)).
+
+### type
+The `type` field can be used to set the type of the info field (This will be reflected in the header of the output VCF file).
+
+### description
+The `description` field can be used to set the description of the info field (This will be reflected in the header of the output VCF file).
+
+### number
+The `number` field can be used to set the number of the info field (This will be reflected in the header of the output VCF file).
+
+### alts
+The `alts` field can be used to set the value of the info field for a specific ALT. The value can be resolved (see [Resolvable fields](#resolvable-fields)).
+
+For example when all `SVLEN` info fields are positive, you maybe want to change the field for all deletions to the negative length:
+```yaml
+info:
+  SVLEN:
+    value: $INFO/SVLEN
+    type: Integer
+    description: "Structural variant length"
+    number: 1
+    alts:
+      DEL: -$INFO/SVLEN
+```
+
+## `format`
+The `format` section can be used to change the format fields for each variant. The `format` section can be defined as follows:
+```yaml
+format:
+  <format_field>:
+    value: <new_value>
+    type: <new_type>
+    description: <new_description>
+    number: <new_number>
+    alts:
+      <alt>: <new_value>
+      <alt>: <new_value>
+```
+
+The format fields work the same as the info fields (see [Info](#info)). 
+
+## Resolvable fields
+
+Some fields can be resolved to a value. 
+
+### Variables
+
+A variable can be resolved appending a `$` to the field name. 
+
+Following variables are available:
+1. `$FORMAT/<format_field>` => This is only accesible for other format fields
+    - An additional `/<number>` can be added to get a specific value in case of multiple values
+2. `$INFO/<info_field>`
+    - An additional `/<number>` can be added to get a specific value in case of multiple values
+3. `$POS`
+4. `$CHROM`
+5. `$ALT`
+6. `$QUAL`
+7. `$FILTER`
+
+For example `$INFO/SVLEN` will be resolved to the value of the `SVLEN` info field.
+
+### Functions
+
+Functions are very simple calculations that can be done on the values.
+
+More functions can be added in the future. Please open an issue to request new functions.
+
+#### `~sub`
+The `~sub` function can be used to substract values from each other. The function can be used as follows:
+
+```yaml
+~sub:<value_start>,<value_to_substract>,<value_to_substract>,...
+```
+
+:warning: only integers and floats are supported for this function :warning:
+
+#### `~sum`
+The `~sum` function can be used to take the sum of all values. The function can be used as follows:
+
+```yaml
+~sum:<value_start>,<value_to_add>,<value_to_add>,...
+```
+
+:warning: only integers and floats are supported for this function :warning:
+
+#### `~len`
+The `~len` function can be used to get the length of a string value. The function can be used as follows:
+
+```yaml
+~len:<value>
+```