make chunk_size param to output_vcf optional

CAST-genomics · Dec 20, 2024 · 2eafd95 · 2eafd95
1 parent d1f7e42
commit 2eafd95
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/haptools/__main__.py b/haptools/__main__.py
@@ -318,8 +318,8 @@ def simgenotype(
             sample_field,
             no_replacement,
             out,
-            chunk_size,
             log,
+            chunk_size,
         )
     end = time.time()
 

diff --git a/haptools/sim_genotype.py b/haptools/sim_genotype.py
@@ -24,8 +24,8 @@ def output_vcf(
         sample_field, 
         no_replacement,
         out,
-        chunk_size,
-        log
+        log,
+        chunk_size = None,
     ):
     """
     Takes in simulated breakpoints and uses reference files, vcf and sampleinfo, 
@@ -71,6 +71,8 @@ def output_vcf(
         output prefix
     log: log object
         Outputs messages to the appropriate channel.
+    chunk_size: int, optional
+        The max number of variants to write to a PGEN file together
     """
 
     log.info(f"Outputting file {out}")