Add sample_query_options to plot_xpehh_gwss(), xpehh_gwss(), plot_xpehh_gwss_track()

Author: leehart

malariagen_data/anopheles.py

@@ -2253,6 +2253,7 @@ def plot_xpehh_gwss(
         sample_sets: Optional[base_params.sample_sets] = None,
         cohort1_query: Optional[base_params.sample_query] = None,
         cohort2_query: Optional[base_params.sample_query] = None,
+        sample_query_options: Optional[base_params.sample_query_options] = None,
         window_size: xpehh_params.window_size = xpehh_params.window_size_default,
         percentiles: xpehh_params.percentiles = xpehh_params.percentiles_default,
         filter_min_maf: xpehh_params.filter_min_maf = xpehh_params.filter_min_maf_default,
@@ -2287,6 +2288,7 @@ def plot_xpehh_gwss(
             sample_sets=sample_sets,
             cohort1_query=cohort1_query,
             cohort2_query=cohort2_query,
+            sample_query_options=sample_query_options,
             window_size=window_size,
             percentiles=percentiles,
             palette=palette,
@@ -2457,6 +2459,7 @@ def xpehh_gwss(
         sample_sets: Optional[base_params.sample_sets] = None,
         cohort1_query: Optional[base_params.sample_query] = None,
         cohort2_query: Optional[base_params.sample_query] = None,
+        sample_query_options: Optional[base_params.sample_query_options] = None,
         window_size: xpehh_params.window_size = xpehh_params.window_size_default,
         percentiles: xpehh_params.percentiles = xpehh_params.percentiles_default,
         filter_min_maf: xpehh_params.filter_min_maf = xpehh_params.filter_min_maf_default,
@@ -2498,6 +2501,7 @@ def xpehh_gwss(
             # are different in the haplotype data.
             cohort1_query=cohort1_query,
             cohort2_query=cohort2_query,
+            sample_query_options=sample_query_options,
             min_cohort_size=min_cohort_size,
             max_cohort_size=max_cohort_size,
             random_seed=random_seed,
@@ -2525,6 +2529,7 @@ def _xpehh_gwss(
         sample_sets,
         cohort1_query,
         cohort2_query,
+        sample_query_options,
         window_size,
         percentiles,
         filter_min_maf,
@@ -2544,6 +2549,7 @@ def _xpehh_gwss(
             region=contig,
             analysis=analysis,
             sample_query=cohort1_query,
+            sample_query_options=sample_query_options,
             sample_sets=sample_sets,
             min_cohort_size=min_cohort_size,
             max_cohort_size=max_cohort_size,
@@ -2556,6 +2562,7 @@ def _xpehh_gwss(
             region=contig,
             analysis=analysis,
             sample_query=cohort2_query,
+            sample_query_options=sample_query_options,
             sample_sets=sample_sets,
             min_cohort_size=min_cohort_size,
             max_cohort_size=max_cohort_size,
@@ -2628,6 +2635,7 @@ def plot_xpehh_gwss_track(
         sample_sets: Optional[base_params.sample_sets] = None,
         cohort1_query: Optional[base_params.sample_query] = None,
         cohort2_query: Optional[base_params.sample_query] = None,
+        sample_query_options: Optional[base_params.sample_query_options] = None,
         window_size: xpehh_params.window_size = xpehh_params.window_size_default,
         percentiles: xpehh_params.percentiles = xpehh_params.percentiles_default,
         filter_min_maf: xpehh_params.filter_min_maf = xpehh_params.filter_min_maf_default,
@@ -2672,6 +2680,7 @@ def plot_xpehh_gwss_track(
             max_cohort_size=max_cohort_size,
             cohort1_query=cohort1_query,
             cohort2_query=cohort2_query,
+            sample_query_options=sample_query_options,
             sample_sets=sample_sets,
             random_seed=random_seed,
             chunks=chunks,