Make it the default behavior to prefer genomic mappings when available

sallybg · sallybg · commit 0b68f5aecbbf · 2025-02-13T13:43:22.000-08:00
diff --git a/src/dcd_mapping/cli.py b/src/dcd_mapping/cli.py
@@ -44,7 +44,7 @@
 @click.option(
     "--prefer_genomic",
     is_flag=True,
-    default=False,
+    default=True,
     help="If mapped variants are available relative to a genomic sequence, only output the genomic mappings",
 )
 def cli(

Original file line number	Diff line number	Diff line change
`@@ -44,7 +44,7 @@`
`44`	`44`	`@click.option(`
`45`	`45`	`"--prefer_genomic",`
`46`	`46`	`is_flag=True,`
`47`		`- default=False,`
	`47`	`+ default=True,`
`48`	`48`	`help="If mapped variants are available relative to a genomic sequence, only output the genomic mappings",`
`49`	`49`	`)`
`50`	`50`	`def cli(`