Bump version to 0.8.0

PlantandFoodResearch · Jan 10, 2023 · d7908d9 · d7908d9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,11 +2,15 @@
 
 ## Unreleased 
 
+
+## Beta v0.8.0
+
 New Features:
 - Combine `--bam`, `--bam-list` and `--sample-bam` arguments #128
 - Combine `--ploidy` and `--sample-ploidy` arguments #128
 - Combine `--inbreeding` and `--sample-inbreeding` arguments #128
 - Combine `--mcmc-temperatures` and `--sample-mcmc-temperatures` arguments #128
+- Improvements to documentation
 
 
 

diff --git a/docs/assemble.rst b/docs/assemble.rst
@@ -3,7 +3,7 @@ MCHap assemble
 
 De novo assembly of micro-haplotypes.
 
-*(Last updated for MCHap version 0.7.1)*
+*(Last updated for MCHap version 0.8.0)*
 
 Background
 ----------

diff --git a/docs/call.rst b/docs/call.rst
@@ -3,7 +3,7 @@ MCHap call
 
 Calling genotypes from known haplotypes.
 
-*(Last updated for MCHap version 0.7.1)*
+*(Last updated for MCHap version 0.8.0)*
 
 Background
 ----------

diff --git a/mchap/tests/test_io/data/mock.input.frequencies.vcf b/mchap/tests/test_io/data/mock.input.frequencies.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20220406
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mockup"
 ##randomseed=11

diff --git a/mchap/tests/test_io/data/simple.output.deep.assemble.vcf b/mchap/tests/test_io/data/simple.output.deep.assemble.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap assemble --bam simple.sample1.deep.bam simple.sample2.deep.bam simple.sample3.deep.bam --ploidy 4 --targets simple.bed.gz --variants simple.vcf.gz --reference simple.fasta --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11 --use-assembly-posteriors"
 ##randomseed=11

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.assemble.frequencies.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.assemble.frequencies.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20220406
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap assemble --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --targets simple.bed.gz --variants simple.vcf.gz --reference simple.fasta --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11 --report AFP"
 ##randomseed=11

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.assemble.pool.frequencies.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.assemble.pool.frequencies.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20220412
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap assemble --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --targets simple.bed.gz --variants simple.vcf.gz --reference simple.fasta --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11 --read-group-field POOL --report AFP"
 ##randomseed=11

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.assemble.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.assemble.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap assemble --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --targets simple.bed.gz --variants simple.vcf.gz --reference simple.fasta --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11"
 ##randomseed=11

diff --git a/...sts/test_io/data/simple.output.mixed_depth.call-exact.frequencies.posteriors.skiprare.vcf b/...sts/test_io/data/simple.output.mixed_depth.call-exact.frequencies.posteriors.skiprare.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20220406
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call-exact --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes mock.input.frequencies.vcf --haplotype-frequencies AFP --skip-rare-haplotypes 0.1 --report AFP GP"
 ##randomseed=None

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.frequencies.prior.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.frequencies.prior.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call-exact --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes mock.input.frequencies.vcf --haplotype-frequencies AFP --haplotype-frequencies-prior --report AFPRIOR AFP"
 ##randomseed=None

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.frequencies.skiprare.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.frequencies.skiprare.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20220406
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call-exact --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes mock.input.frequencies.vcf --haplotype-frequencies AFP --skip-rare-haplotypes 0.1 --report AFP"
 ##randomseed=None

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.frequencies.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.frequencies.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20220406
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call-exact --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes simple.output.mixed_depth.assemble.vcf --report AFP"
 ##randomseed=None

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.likelihoods.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.likelihoods.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call-exact --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes simple.output.mixed_depth.assemble.vcf --genotype-likelihoods"
 ##randomseed=None

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.posteriors.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.posteriors.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call-exact --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes simple.output.mixed_depth.assemble.vcf --genotype-posteriors"
 ##randomseed=None

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call-exact.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call-exact --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes simple.output.mixed_depth.assemble.vcf"
 ##randomseed=None

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call.frequencies.prior.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call.frequencies.prior.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes mock.input.frequencies.vcf --haplotype-frequencies AFP --haplotype-frequencies-prior --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11 --report AFPRIOR AFP"
 ##randomseed=11

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call.frequencies.skiprare.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call.frequencies.skiprare.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20220406
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes mock.input.frequencies.vcf --haplotype-frequencies AFP --skip-rare-haplotypes 0.1 --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11 --report AFP"
 ##randomseed=11

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call.frequencies.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call.frequencies.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20220406
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes simple.output.deep.assemble.vcf --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11 --report AFP"
 ##randomseed=11

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call.likelihoods.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call.likelihoods.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes simple.output.mixed_depth.assemble.vcf --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11 --genotype-likelihoods"
 ##randomseed=11

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call.posteriors.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call.posteriors.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes simple.output.mixed_depth.assemble.vcf --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11 --genotype-posteriors"
 ##randomseed=11

diff --git a/mchap/tests/test_io/data/simple.output.mixed_depth.call.vcf b/mchap/tests/test_io/data/simple.output.mixed_depth.call.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap call --bam simple.sample1.bam simple.sample2.deep.bam simple.sample3.bam --ploidy 4 --haplotypes simple.output.mixed_depth.assemble.vcf --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11"
 ##randomseed=11

diff --git a/mchap/tests/test_io/data/simple.output.nullallele.assemble.vcf b/mchap/tests/test_io/data/simple.output.nullallele.assemble.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.3
 ##fileDate=20210420
-##source=mchap v0.7.0
+##source=mchap v0.8.0
 ##phasing=None
 ##commandline="mchap assemble --bam simple.sample1.bam simple.sample2.bam simple.sample3.bam --ploidy 4 --targets simple.bed.gz --variants simple.vcf.gz --reference simple.fasta --mcmc-steps 500 --mcmc-burn 100 --mcmc-seed 11 --haplotype-posterior-threshold 1.0"
 ##randomseed=11

diff --git a/mchap/version.py b/mchap/version.py
@@ -1 +1 @@
-__version__ = "0.7.0"
+__version__ = "0.8.0"