Merge pull request #184 from timothymillar/atomize

Beta v0.10.0

.github/workflows/python-package.yml

@@ -5,17 +5,17 @@ name: Python package
 
 on:
   push:
-    branches: [ master ]
+    branches: [ master, "call-pedigree"]
   pull_request:
-    branches: [ master ]
+    branches: [ master, "call-pedigree"]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2
@@ -32,8 +32,7 @@ jobs:
       uses: pre-commit/[email protected]
     - name: Build and install mchap
       run: |
-        python setup.py sdist
-        pip install dist/mchap-*.tar.gz
+        pip install .
     - name: Test with pytest (bounds checked)
       env:
         NUMBA_BOUNDSCHECK: 1

CHANGELOG.md

@@ -3,6 +3,24 @@
 ## Unreleased 
 
 
+## Beta v0.10.0 
+
+New Features:
+- New experimental `atomize` tool for splitting haplotypes into basis SNVs #72. 
+- New experimental `call-pedigree` tool fo pedigree informed genotype calling.
+- Optionally specify just the `INFO` or `FORMAT` variant of a optional VCF field.
+- Use `setuptools_scm` for versioning #179.
+
+VCF Changes:
+- Renamed `PHQ` and `PHPM` to `SQ` and `SPM` for clarity.
+- Added `INFO/UAN` field for number of unique alleles called #174.
+- Added `INFO/MCI` field for proportion of sample with Markov Chain incongruence.
+- Added optional fields #174:
+    * `INFO/AOPSUM` (sum of `FORMAT/AOP`).
+    * `INFO/ACP` and `FORMAT/ACP`.
+    * `INFO/SNVDP` and `FORMAT/SNVDP`.
+
+
 ## Beta v0.9.3
 
 Bug Fixes:

README.rst

@@ -66,7 +66,17 @@ frequencies (estimated from the mean of individual frequencies), but no genotype
 Example notebook
 ----------------
 
-An `example notebook`_ demonstrating genotype calling with MCHap in a bi-parental population.
+See the `example notebook`_ demonstrating genotype calling with MCHap in a bi-parental population.
+
+Experimental features
+---------------------
+
+    \:warning: **WARNING: The following tools are highly experimental!!!** :warning:
+
+- ``mchap call-pedigree``: for pedigree informed genotype calling.
+- ``mchap atomize``: for converting micro-haplotype calls to phased sets of SNVs.
+
+See the `experimental notebook`_ demonstrating the `call-pedigree` tool as presented at the 2024 `Tools for Polyploids`_ workshop.
 
 Funding
 -------
@@ -80,3 +90,5 @@ The development of MCHap was partially funded by the "Tools for Polyploids" Spec
 .. _`MCHap assemble documentation`: docs/assemble.rst
 .. _`MCHap call documentation`: docs/call.rst
 .. _`example notebook`: docs/example/bi-parental.ipynb
+.. _`experimental notebook`: docs/example/bi-parental-pedigree.ipynb
+.. _`Tools for Polyploids`: https://www.polyploids.org/

cli-assemble-help.txt

@@ -115,11 +115,21 @@ options:
                         The chosen field determines tha sample ids required in
                         other input files e.g. the --sample-list argument.
   --report [REPORT ...]
-                        Extra fields to report within the output VCF: AFPRIOR
-                        = prior allele frequencies; AFP = posterior mean
-                        allele frequencies; AOP = posterior probability of
-                        allele occurring at any copy number; GP = genotype
-                        posterior probabilities; GL = genotype likelihoods.
+                        Extra fields to report within the output VCF. The
+                        INFO/FORMAT prefix may be omitted to return both
+                        variations of the named field. Options include:
+                        INFO/AFPRIOR = Prior allele frequencies; INFO/ACP =
+                        Posterior allele counts; INFO/AFP = Posterior mean
+                        allele frequencies; INFO/AOP = Posterior probability
+                        of allele occurring across all samples; INFO/AOPSUM =
+                        Posterior estimate of the number of samples containing
+                        an allele; INFO/SNVDP = Read depth at each SNV
+                        position; FORMAT/ACP: Posterior allele counts;
+                        FORMAT/AFP: Posterior mean allele frequencies;
+                        FORMAT/AOP: Posterior probability of allele occurring;
+                        FORMAT/GP: Genotype posterior probabilities;
+                        FORMAT/GL: Genotype likelihoods; FORMAT/SNVDP: Read
+                        depth at each SNV position
   --cores CORES         Number of cpu cores to use (default = 1).
   --mcmc-chains MCMC_CHAINS
                         Number of independent MCMC chains per assembly
@@ -133,9 +143,8 @@ options:
   --mcmc-seed MCMC_SEED
                         Random seed for MCMC (default = 42).
   --mcmc-chain-incongruence-threshold MCMC_CHAIN_INCONGRUENCE_THRESHOLD
-                        Posterior phenotype probability threshold for
-                        identification of incongruent posterior modes (default
-                        = 0.60).
+                        Posterior probability threshold for identification of
+                        incongruent posterior modes (default = 0.60).
   --mcmc-fix-homozygous MCMC_FIX_HOMOZYGOUS
                         Fix alleles that are homozygous with a probability
                         greater than or equal to the specified value (default

cli-atomize-help.txt

@@ -0,0 +1,15 @@
+usage: Split MCHap haplotype calls into phased blocks of basis SNVs.
+       [-h] haplotypes
+
+positional arguments:
+  haplotypes  VCF file containing haplotype variants to be atomized. This file
+              must contain INFO/SNVPOS. The INFO/DP and FORMAT/DP fields will
+              be calculated from FORMAT/SNVDP if present in the input VCF
+              file. The INFO/ACP and FORMAT/DS fields will be calculated from
+              FORMAT/ACP or FORMAT/AFP if either is present in the input VCF
+              file. Note that the FORMAT/ACP or FORMAT/AFP fields from the
+              input VCF file will be normalized in the event that they do not
+              sum to ploidy or one respectively.
+
+options:
+  -h, --help  show this help message and exit

cli-call-exact-help.txt

@@ -102,9 +102,19 @@ options:
                         The chosen field determines tha sample ids required in
                         other input files e.g. the --sample-list argument.
   --report [REPORT ...]
-                        Extra fields to report within the output VCF: AFPRIOR
-                        = prior allele frequencies; AFP = posterior mean
-                        allele frequencies; AOP = posterior probability of
-                        allele occurring at any copy number; GP = genotype
-                        posterior probabilities; GL = genotype likelihoods.
+                        Extra fields to report within the output VCF. The
+                        INFO/FORMAT prefix may be omitted to return both
+                        variations of the named field. Options include:
+                        INFO/AFPRIOR = Prior allele frequencies; INFO/ACP =
+                        Posterior allele counts; INFO/AFP = Posterior mean
+                        allele frequencies; INFO/AOP = Posterior probability
+                        of allele occurring across all samples; INFO/AOPSUM =
+                        Posterior estimate of the number of samples containing
+                        an allele; INFO/SNVDP = Read depth at each SNV
+                        position; FORMAT/ACP: Posterior allele counts;
+                        FORMAT/AFP: Posterior mean allele frequencies;
+                        FORMAT/AOP: Posterior probability of allele occurring;
+                        FORMAT/GP: Genotype posterior probabilities;
+                        FORMAT/GL: Genotype likelihoods; FORMAT/SNVDP: Read
+                        depth at each SNV position
   --cores CORES         Number of cpu cores to use (default = 1).

cli-call-help.txt

@@ -106,11 +106,21 @@ options:
                         The chosen field determines tha sample ids required in
                         other input files e.g. the --sample-list argument.
   --report [REPORT ...]
-                        Extra fields to report within the output VCF: AFPRIOR
-                        = prior allele frequencies; AFP = posterior mean
-                        allele frequencies; AOP = posterior probability of
-                        allele occurring at any copy number; GP = genotype
-                        posterior probabilities; GL = genotype likelihoods.
+                        Extra fields to report within the output VCF. The
+                        INFO/FORMAT prefix may be omitted to return both
+                        variations of the named field. Options include:
+                        INFO/AFPRIOR = Prior allele frequencies; INFO/ACP =
+                        Posterior allele counts; INFO/AFP = Posterior mean
+                        allele frequencies; INFO/AOP = Posterior probability
+                        of allele occurring across all samples; INFO/AOPSUM =
+                        Posterior estimate of the number of samples containing
+                        an allele; INFO/SNVDP = Read depth at each SNV
+                        position; FORMAT/ACP: Posterior allele counts;
+                        FORMAT/AFP: Posterior mean allele frequencies;
+                        FORMAT/AOP: Posterior probability of allele occurring;
+                        FORMAT/GP: Genotype posterior probabilities;
+                        FORMAT/GL: Genotype likelihoods; FORMAT/SNVDP: Read
+                        depth at each SNV position
   --cores CORES         Number of cpu cores to use (default = 1).
   --mcmc-chains MCMC_CHAINS
                         Number of independent MCMC chains per assembly
@@ -124,6 +134,5 @@ options:
   --mcmc-seed MCMC_SEED
                         Random seed for MCMC (default = 42).
   --mcmc-chain-incongruence-threshold MCMC_CHAIN_INCONGRUENCE_THRESHOLD
-                        Posterior phenotype probability threshold for
-                        identification of incongruent posterior modes (default
-                        = 0.60).
+                        Posterior probability threshold for identification of
+                        incongruent posterior modes (default = 0.60).