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Beta v0.10.0 #184

Merged
merged 84 commits into from
Sep 18, 2024
Merged

Beta v0.10.0 #184

merged 84 commits into from
Sep 18, 2024

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timothymillar
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New Features:

  • New experimental atomize tool for splitting haplotypes into basis SNVs Atomize VCF script #72.
  • New experimental call-pedigree tool fo pedigree informed genotype calling.
  • Optionally specify just the INFO or FORMAT variant of an optional VCF field Additional info fields #174.
  • Use setuptools_scm for versioning version #179.
  • Added example notebook from 2024 Tools for Polyploids workshop.

VCF Changes:

  • Renamed PHQ and PHPM to SQ and SPM for clarity.
  • Added INFO/UAN field for number of unique alleles called Additional info fields #174.
  • Added INFO/MCI field for proportion of sample with Markov Chain incongruence.
  • Added optional fields Additional info fields #174:
    • INFO/AOPSUM (sum of FORMAT/AOP).
    • INFO/ACP and FORMAT/ACP.
    • INFO/SNVDP and FORMAT/SNVDP.

timothymillar added 30 commits May 9, 2024 11:05
@timothymillar
Use scm for versioning and -v to get version PlantandFoodResearch#179
6032359
@timothymillar
Add more optional --report fields PlantandFoodResearch#174
f3fabf9 
- Allow specification of INFO and FORMAT field variants
- Add ACP field
- Add INFO/AOPSUM field
- Add SNVDP field
@timothymillar
Improve handeling of INFO and FORMAT fields
831f108 
- Use objects rather than strings for fields
- Use constants for columns
- Store reads in seperate dataclass fields
- Round floats as part of string formatting
- Move MEC calculation to subclasses
@timothymillar
Add UAN and MCI INFO fields
a577a49
@timothymillar
Rename fields PHQ and PHPM to SQ and SPM
4f1b6b2
@timothymillar
Test AOPSUM with AOP
dbf1c3e
@timothymillar
Test SNVDP optional field
c99d2fa
@timothymillar
Add tests for optional ACP fields
d08bec0
@timothymillar
Update CLI help text
b81daa0
@timothymillar
Update docs
f398441
@timothymillar
Update example
498f6b2
@timothymillar
Changelog
0237a1e
@timothymillar
Initial pedigree submodule
ac71155
@timothymillar
Correct PMF for second gamete of unknown origin
eb28099
@timothymillar
Docstrings
3265e67
@timothymillar
Rename pedigree sampler and add docstring
7563915
@timothymillar
Ensure zero-count reads removed from likelihood function
40f5f24
@timothymillar
Introduce H-K lambda parameter for diploid gametes
cb84a02
@timothymillar
Tests
9c53f8c
@timothymillar
Tests for log_gamete_pmf
9f11db8
@timothymillar
Test second_gamete_log_pmf
1a96491
@timothymillar
Reorder test perms
76aeae0
@timothymillar
Initial PedigreeCallingMCMC class
cf2d5d3
@timothymillar
Initial call-pedigree CLI
d6b9a72
@timothymillar
Report pedigree posterior error PEDERR
8d37298
@timothymillar
Test pedigree validation
b608eec
@timothymillar
Improve ploidy and inbreeding handeling with pedigree
33f3e78
@timothymillar
Note to handle read io for dummy samples
2341e8f
@timothymillar
Seperate out mh-probabilities function
38d7104
@timothymillar
Simplify use of lambda in gamete PMF
fe07831
timothymillar and others added 20 commits July 9, 2024 15:57
@timothymillar timothymillar force-pushed the atomize branch 7 times, most recently from ce771cb to fe219f8 Compare September 18, 2024 22:35
@timothymillar timothymillar merged commit 29935f7 into PlantandFoodResearch:master Sep 18, 2024
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@timothymillar @rfinkers