scan remove chrM

src/scan/scan.rs

@@ -529,12 +529,10 @@ pub fn scan_contig(
 
         let fb_positions: [Option<u32>; 2] =
             if let Some(inv) = fb_inv_from_record(rec, &header, min_mapq, Some(150), Some(200)) {
-                let a_end_minus_1 = (inv.aln_a_end > 0
-                    && (inv.aln_a_end - 1) < contig_len as i64)
+                let a_end_minus_1 = (inv.aln_a_end > 0 && (inv.aln_a_end - 1) < contig_len as i64)
                     .then_some((inv.aln_a_end - 1) as u32);
 
-                let b_start = (inv.aln_b_start >= 0
-                    && inv.aln_b_start < contig_len as i64)
+                let b_start = (inv.aln_b_start >= 0 && inv.aln_b_start < contig_len as i64)
                     .then_some(inv.aln_b_start as u32);
 
                 [a_end_minus_1, b_start]
@@ -542,7 +540,6 @@ pub fn scan_contig(
                 [None, None]
             };
 
-
         // "last wins" representative per qname (same as HashMap overwrite behavior)
         let qname = rec.qname().to_vec();
 
@@ -567,7 +564,6 @@ pub fn scan_contig(
                 if is_lowq {
                     b.lowq[i] += 1;
                 }
-                
             }
 
             for pos in fb_positions.into_iter().flatten() {
@@ -698,6 +694,7 @@ pub fn par_whole_scan(id: &str, time_point: &str, config: &Config) -> anyhow::Re
     let header = bam::Header::from_template(reader.header());
     let contigs: Vec<(String, u32)> = get_genome_sizes(&header)?
         .into_iter()
+        .filter(|(ctg, _)| ctg != "chrM")
         .map(|(ctg, len)| {
             u32::try_from(len)
                 .map(|l| (ctg.clone(), l))