Add sample_query_options to h1x_gwss()

Author: leehart

malariagen_data/anoph/h1x.py

@@ -32,6 +32,7 @@ def _h1x_gwss(
         sample_sets,
         cohort1_query,
         cohort2_query,
+        sample_query_options,
         cohort_size,
         min_cohort_size,
         max_cohort_size,
@@ -44,6 +45,7 @@ def _h1x_gwss(
             region=contig,
             analysis=analysis,
             sample_query=cohort1_query,
+            sample_query_options=sample_query_options,
             sample_sets=sample_sets,
             cohort_size=cohort_size,
             min_cohort_size=min_cohort_size,
@@ -56,6 +58,7 @@ def _h1x_gwss(
             region=contig,
             analysis=analysis,
             sample_query=cohort2_query,
+            sample_query_options=sample_query_options,
             sample_sets=sample_sets,
             cohort_size=cohort_size,
             min_cohort_size=min_cohort_size,
@@ -102,6 +105,7 @@ def h1x_gwss(
         window_size: h12_params.window_size,
         cohort1_query: base_params.sample_query,
         cohort2_query: base_params.sample_query,
+        sample_query_options: base_params.sample_query_options,
         analysis: hap_params.analysis = base_params.DEFAULT,
         sample_sets: Optional[base_params.sample_sets] = None,
         cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default,
@@ -128,6 +132,7 @@ def h1x_gwss(
             # are different in the haplotype data.
             cohort1_query=cohort1_query,
             cohort2_query=cohort2_query,
+            sample_query_options=sample_query_options,
             sample_sets=self._prep_sample_sets_param(sample_sets=sample_sets),
             cohort_size=cohort_size,
             min_cohort_size=min_cohort_size,