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Merged
zrm22 merged 10 commits into from
Dec 12, 2025
Merged

Ref based sim #5

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087bf51
Initial commit of Ref Based fast mutation code
zrm22 Dec 4, 2025
9f7e526
Add more unit tests
zrm22 Dec 5, 2025
202f971
Additional updates for mutation code
zrm22 Dec 5, 2025
82a60ad
Initial gvcf output
zrm22 Dec 9, 2025
651af14
Refactor to make some things easier to test
zrm22 Dec 10, 2025
a9b1feb
Adding more unit testing
zrm22 Dec 10, 2025
8432709
Adding more unit tests
zrm22 Dec 11, 2025
a6a9997
Adding unit test files and updating gitignore
zrm22 Dec 11, 2025
fd246cc
Merge branch 'main' into ref-based-sim
zrm22 Dec 12, 2025
d8314a3
Updating version
zrm22 Dec 12, 2025
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2 changes: 1 addition & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ build/
.idea/jarRepositories.xml
.idea/compiler.xml
.idea/libraries/
.idea
*.iws
*.iml
*.ipr
Expand Down Expand Up @@ -55,7 +56,6 @@ CLAUDE.md
### Project specific ###
seq_sim_work/
scripts/align25pairs.sh
data/

### Pixi environment ###
pixi.lock
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7 changes: 6 additions & 1 deletion build.gradle.kts
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Expand Up @@ -4,7 +4,7 @@ plugins {
}

group = "net.maizegenetics"
version = "0.2.1"
version = "0.2.2"

repositories {
mavenCentral()
Expand All @@ -15,6 +15,11 @@ dependencies {
implementation("org.apache.logging.log4j:log4j-api:2.24.3")
implementation("org.apache.logging.log4j:log4j-core:2.24.3")
implementation("org.yaml:snakeyaml:2.3")
implementation("org.biokotlin:biokotlin:1.0.0")
implementation("com.google.guava:guava:33.1.0-jre")
implementation("com.github.samtools:htsjdk:4.0.1")


testImplementation(kotlin("test"))
}

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22 changes: 22 additions & 0 deletions data/MutateAssemblies/founder.g.vcf
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@@ -0,0 +1,22 @@
##fileformat=VCFv4.2
##FORMAT=<ID=AD,Number=3,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AF,Number=3,Type=Integer,Description="Allele Frequency">
##INFO=<ID=ASM_Chr,Number=1,Type=String,Description="Assembly chromosome">
##INFO=<ID=ASM_End,Number=1,Type=Integer,Description="Assembly end position">
##INFO=<ID=ASM_Start,Number=1,Type=Integer,Description="Assembly start position">
##INFO=<ID=ASM_Strand,Number=1,Type=String,Description="Assembly strand">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT loadingTest
chr1 100 . A <NON_REF> . . END=150 GT 0/0
chr1 150 . C G . . END=150 GT 1/1
chr1 151 . T <NON_REF> . . END=200 GT 0/0
chr1 201 . GGGGG G . . END=205 GT 1/1
chr1 206 . A <NON_REF> . . END=300 GT 0/0
chr1 301 . G C . . END=301 GT 1/1
chr1 302 . T <NON_REF> . . END=400 GT 0/0
18 changes: 18 additions & 0 deletions data/MutateAssemblies/nonFounder.g.vcf
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@@ -0,0 +1,18 @@
##fileformat=VCFv4.2
##FORMAT=<ID=AD,Number=3,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AF,Number=3,Type=Integer,Description="Allele Frequency">
##INFO=<ID=ASM_Chr,Number=1,Type=String,Description="Assembly chromosome">
##INFO=<ID=ASM_End,Number=1,Type=Integer,Description="Assembly end position">
##INFO=<ID=ASM_Start,Number=1,Type=Integer,Description="Assembly start position">
##INFO=<ID=ASM_Strand,Number=1,Type=String,Description="Assembly strand">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT loadingTest
chr1 125 . T A . . END=125 GT 1/1
chr1 175 . C TTTT . . END=175 GT 1/1
chr1 500 . A T . . END=500 GT 1/1
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