first commit

.gitignore

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+
+# Created by https://www.gitignore.io/api/python
+# Edit at https://www.gitignore.io/?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don’t work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# vscode
+.vscode/
+
+# poetry
+poetry.lock
+
+# backup file
+*.bak
+
+# End of https://www.gitignore.io/api/python
+
+examples/*.R
+examples/*.txt

Makefile

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+TARGETS :=  examples/Number_of_variants_on_each_chromosome.col.png \
+			examples/Number_of_variants_on_each_chromosome_(modified).col.png \
+			examples/Number_of_variants_on_each_chromosome_(first_5).col.png \
+			examples/Number_of_substitutions_of_SNPs.col.png \
+			examples/Number_of_substitutions_of_SNPs_(passed).col.png \
+			examples/Allele_frequency_on_each_chromosome.violin.png \
+			examples/Allele_frequency_on_each_chromosome.boxplot.png \
+			examples/Allele_frequency_on_chromosome_1_2.density.png \
+			examples/Overall_allele_frequency_distribution.histogram.png \
+			examples/Overall_allele_frequency_distribution_(0.05-0.95).histogram.png \
+			examples/Distribution_of_allele_frequency_on_chromosome_1.histogram.png \
+			examples/Types_of_variants_on_each_chromosome.col.png \
+			examples/Types_of_variants_on_each_chromosome_1.pie.png \
+			examples/Types_of_variants_on_whole_genome.pie.png \
+			examples/Allele_frequency_vs_depth_(sample_1).scatter.png \
+			examples/Mutant_genotypes_on_each_chromosome_(sample_1).col.png \
+			examples/Allele_frequency_vs_depth_(sample_1).scatter.png \
+			examples/Depths_between_sample_1_and_2.scatter.png
+
+
+DEPENDS :=  examples/sample.vcf examples/config.toml vcfstats/__init__.py \
+			vcfstats/formula.py vcfstats/macros.py vcfstats/one.py
+
+VCFSTATS := vcfstats --vcf examples/sample.vcf \
+	--outdir examples/ \
+	--config examples/config.toml
+
+FILETOTITLE = $(subst _, ,$(notdir $(basename $(basename $(1)))))
+FIGTYPE = $(patsubst .%,%,$(suffix $(basename $(notdir $(1)))))
+LOGGER = $(info $(empty))$(info \# Working on '$(call FILETOTITLE,$(1))' ...)\
+		 $(info ===================================================================================)
+
+.PHONY: all clean
+
+all: $(TARGETS)
+
+examples/Types_of_variants_on_whole_genome.col.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+
+
+examples/Number_of_variants_on_each_chromosome.col.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'COUNT(1) ~ CONTIG'
+
+examples/Number_of_variants_on_each_chromosome_(modified).col.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'COUNT(1) ~ CONTIG' \
+	--ggs 'scale_x_discrete(name ="Chromosome", limits=c("1","2","3","4","5","6","7","8","9","10","X")) + ylab("# Variants")'
+
+examples/Number_of_substitutions_of_SNPs.col.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'COUNT(1, VARTYPE[snp]) ~ SUBST[A>T,A>G,A>C,T>A,T>G,T>C,G>A,G>T,G>C,C>A,C>T,C>G]' \
+
+examples/Number_of_substitutions_of_SNPs_(passed).col.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'COUNT(1, VARTYPE[snp]) ~ SUBST[A>T,A>G,A>C,T>A,T>G,T>C,G>A,G>T,G>C,C>A,C>T,C>G]' \
+	--passed
+
+examples/Number_of_variants_on_each_chromosome_(first_5).col.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'COUNT(1) ~ CONTIG[1-5]'
+
+examples/Allele_frequency_on_each_chromosome.violin.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'AAF ~ CONTIG' \
+	--ggs 'theme_dark()'
+
+examples/Allele_frequency_on_each_chromosome.boxplot.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'AAF ~ CONTIG'
+
+examples/Allele_frequency_on_chromosome_1_2.density.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'AAF ~ CONTIG[1,2]' \
+	--figtype density
+
+examples/Overall_allele_frequency_distribution.histogram.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'AAF ~ 1'
+
+examples/Overall_allele_frequency_distribution_(0.05-0.95).histogram.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'AAF[0.05, 0.95] ~ 1'
+
+examples/Distribution_of_allele_frequency_on_chromosome_1.histogram.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'AAF ~ CHROM[1]'
+
+examples/Types_of_variants_on_each_chromosome.col.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'COUNT(1, group=VARTYPE) ~ CHROM'
+
+examples/Types_of_variants_on_each_chromosome_1.pie.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'COUNT(1, group=VARTYPE) ~ CHROM[1]' \
+	--figtype pie
+
+examples/Types_of_variants_on_whole_genome.pie.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'COUNT(1, group=VARTYPE) ~ 1'
+
+examples/Allele_frequency_vs_depth_(sample_1).scatter.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'MEAN(AFs{0}) ~ MEAN(DEPTHs{0}, group=CHROM)'
+
+examples/Mutant_genotypes_on_each_chromosome_(sample_1).col.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'COUNT(1, group=GTTYPEs[HET,HOM_ALT]{0}) ~ CHROM'
+
+examples/Depths_between_sample_1_and_2.scatter.png: $(DEPENDS)
+	@$(call LOGGER,$@)
+	$(VCFSTATS) --title '$(call FILETOTITLE,$@)' --figtype $(call FIGTYPE,$@) \
+	--formula 'DEPTHs{0} ~ DEPTHs{1}'
+
+clean:
+	rm -f examples/*.txt examples/*.R examples/*.png