dysgu_dev <- master (#108)

* correct usage of update_filter_value in filter_normals

It seems like at some point the usage of update_filter_value changed, because in several spots, it is missing the sample_name argument. This breaks `dysgu filter --keep-all`.

* Update main.yml

* Update main.yml

* Update requirements.txt

* updated build process to pyproject.toml (#103)

* v1.6.6 updated README

* Update main.yml

* Added pyproject.toml

* Updated pyproject.toml and setup.py

* Update pyproject.toml

---------

Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com>

dysgu/filter_normals.py

@@ -1025,13 +1025,13 @@ def run_filtering(args):
         if mq_pri < min_mapq and mq_sup < min_mapq:
             filter_results['lowMapQ'] += 1
             if keep_all:
-                update_filter_value(r, old_filter_value, pass_prob, new_value="lowMapQ")
+                update_filter_value(r, sample_name, old_filter_value, pass_prob, new_value="lowMapQ")
                 out_vcf.write(r)
             continue
         if min_prob != 0 and 'PROB' in r.samples[sample_name] and r.samples[sample_name]['PROB'] < min_prob:
             filter_results['lowProb'] += 1
             if keep_all:
-                update_filter_value(r, old_filter_value, pass_prob, new_value="lowProb")
+                update_filter_value(r, sample_name, old_filter_value, pass_prob, new_value="lowProb")
                 out_vcf.write(r)
             continue
         if has_low_support(r, sample_name, support_fraction):

pyproject.toml

@@ -34,13 +34,6 @@ dependencies = [
 [project.urls]
 Homepage = "https://github.com/kcleal/dysgu"
 
-[project.optional-dependencies]
-test = [
-    "pytest",
-    "pytest-cov",
-    "pytest-mock",
-]
-
 [project.scripts]
 dysgu = "dysgu.main:cli"
 

requirements.txt

@@ -1,5 +1,5 @@
 setuptools>=63.0
-cython
+Cython
 click>=8.0
 numpy
 scipy