From a98c06411dc19e443b7d6e519271150aebfff804 Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mrvollger@gmail.com>
Date: Fri, 15 Dec 2023 10:14:01 -0800
Subject: [PATCH] add skip no m6a opts

---
 src/cli.rs  | 3 +++
 src/fire.rs | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/src/cli.rs b/src/cli.rs
index 79fcf4de..327cb21a 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -274,6 +274,9 @@ pub struct FireOptions {
     /// Output just FIRE elements in bed9 format
     #[clap(short, long)]
     pub extract: bool,
+    /// Don't write reads with no m6A calls to the output bam
+    #[clap(short, long)]
+    pub skip_no_m6a: bool,
     /// Width of bin for feature collection
     #[clap(short, long, default_value = "40")]
     pub width_bin: i64,
diff --git a/src/fire.rs b/src/fire.rs
index 524a2103..bc2b4d10 100644
--- a/src/fire.rs
+++ b/src/fire.rs
@@ -519,6 +519,9 @@ pub fn add_fire_to_bam(fire_opts: &FireOptions) -> Result<(), anyhow::Error> {
     else {
         let mut out = bam_writer(&fire_opts.out, &bam, 8);
         for mut rec in FiberseqRecords::new(&mut bam, 0) {
+            if fire_opts.skip_no_m6a && rec.m6a.starts.is_empty() {
+                continue;
+            }
             let fire_feats = FireFeats::new(&rec, fire_opts);
             let mut precisions = fire_feats.predict_with_xgb(&model, &precision_table);
             if rec.record.is_reverse() {