From ee26deae3c8eb1890738286b36a5bf3dc77031a0 Mon Sep 17 00:00:00 2001
From: DonFreed <donfreed12@gmail.com>
Date: Tue, 17 Sep 2024 09:47:34 -0700
Subject: [PATCH] Add `-Y` to minimap2 by default

Expose `--minimap2_args` on the command line.
---
 sentieon_cli/command_strings.py   | 4 ++++
 sentieon_cli/dnascope_longread.py | 9 +++++++++
 2 files changed, 13 insertions(+)

diff --git a/sentieon_cli/command_strings.py b/sentieon_cli/command_strings.py
index 01259d5..8c9e1cc 100644
--- a/sentieon_cli/command_strings.py
+++ b/sentieon_cli/command_strings.py
@@ -260,6 +260,7 @@ def cmd_samtools_fastq_minimap2(
     sample_name: str,
     input_ref: Optional[pathlib.Path] = None,
     fastq_taglist: str = "*",
+    minimap2_args: str = "-Y",
     util_sort_args: str = "--cram_write_options version=3.0,compressor=rans",
 ) -> str:
     """Re-align an input BAM/CRAM/uBAM/uCRAM file with minimap2"""
@@ -288,6 +289,7 @@ def cmd_samtools_fastq_minimap2(
         "-t",
         str(cores),
         "-a",
+        minimap2_args,
         "-x",
         f"{model_bundle}/minimap2.model",
         str(reference),
@@ -434,6 +436,7 @@ def cmd_fastq_minimap2(
     model_bundle: pathlib.Path,
     cores: int,
     unzip: str = "gzip",
+    minimap2_args: str = "-Y",
     util_sort_args: str = "--cram_write_options version=3.0,compressor=rans",
 ) -> str:
     """Align an input fastq file with minimap2"""
@@ -449,6 +452,7 @@ def cmd_fastq_minimap2(
         "-t",
         str(cores),
         "-a",
+        minimap2_args,
         "-x",
         f"{model_bundle}/minimap2.model",
         "-R",
diff --git a/sentieon_cli/dnascope_longread.py b/sentieon_cli/dnascope_longread.py
index efd4a75..be32a48 100644
--- a/sentieon_cli/dnascope_longread.py
+++ b/sentieon_cli/dnascope_longread.py
@@ -72,6 +72,7 @@ def align_inputs(
     skip_version_check: bool = False,
     bam_format: bool = False,
     fastq_taglist: str = "*",
+    minimap2_args: str = "-Y",
     util_sort_args: str = "--cram_write_options version=3.0,compressor=rans",
     input_ref: Optional[pathlib.Path] = None,
     **_kwargs: Any,
@@ -107,6 +108,7 @@ def align_inputs(
                 sample_name,
                 input_ref,
                 fastq_taglist,
+                minimap2_args,
                 util_sort_args,
             )
         )
@@ -124,6 +126,7 @@ def align_fastq(
     readgroups: Optional[List[str]] = None,
     skip_version_check: bool = False,
     bam_format: bool = False,
+    minimap2_args: str = "-Y",
     util_sort_args: str = "--cram_write_options version=3.0,compressor=rans",
     **_kwargs: Any,
 ) -> List[pathlib.Path]:
@@ -166,6 +169,7 @@ def align_fastq(
                 model_bundle,
                 cores,
                 unzip,
+                minimap2_args,
                 util_sort_args,
             )
         )
@@ -726,6 +730,10 @@ def mosdepth(
     help="Use the BAM format instead of CRAM for output aligned files",
     action="store_true",
 )
+@arg(
+    "--minimap2_args",
+    help="Extra arguments for sentieon minimap2",
+)
 @arg(
     "--util_sort_args",
     help="Extra arguments for sentieon util sort",
@@ -766,6 +774,7 @@ def dnascope_longread(
     input_ref: Optional[pathlib.Path] = None,
     fastq_taglist: str = "*",  # pylint: disable=W0613
     bam_format: bool = False,  # pylint: disable=W0613
+    minimap2_args: str = "-Y",  # pylint: disable=W0613
     util_sort_args: str = (
         "--cram_write_options version=3.0,compressor=rans"
     ),  # pylint: disable=W0613