fbinv

src/scan/bin.rs

@@ -5,7 +5,7 @@ use csv::ByteRecord;
 use log::error;
 use rust_htslib::bam::{ext::BamRecordExtensions, record::Aux, IndexedReader, Read, Record};
 
-use crate::io::{bam::{primary_record, primary_records}, tsv::{parse_csv_u32_into, parse_u32}};
+use crate::io::{bam::{fb_inv_from_record, primary_record, primary_records}, tsv::{parse_csv_u32_into, parse_u32}};
 
 /// A genomic bin containing reads from a specific region.
 ///
@@ -30,6 +30,7 @@ pub struct Bin {
     pub low_qualities: Vec<u32>,
     /// Vec of depths
     pub depths: Vec<u32>,
+    pub fb_invs: Vec<u32>,
 }
 
 impl Bin {
@@ -65,10 +66,12 @@ impl Bin {
         bam_reader
             .fetch((contig, start as i64, end as i64))
             .with_context(|| format!("Failed to fetch region {}:{}-{}", contig, start, end))?;
+        let header = bam_reader.header().clone();
 
         let mut reads_store: HashMap<Vec<u8>, Record> = HashMap::new();
         let mut depths = vec![0u32; length as usize]; // Optional pseudo-depth
         let mut low_qualities = vec![0u32; length as usize]; // Optional pseudo-depth
+        let mut fb_invs = vec![0u32; length as usize];
 
         for record_result in bam_reader.rc_records() {
             let rc_record = match record_result {
@@ -102,6 +105,9 @@ impl Bin {
                         if record.mapq() < min_mapq {
                             low_qualities[i] += 1;
                         }
+                        if let Some(_fbinv) = fb_inv_from_record(record, &header, min_mapq, Some(150), Some(200)) {
+                            fb_invs[i] += 1;
+                        }
                     }
                 }
             }
@@ -114,6 +120,7 @@ impl Bin {
             reads_store,
             low_qualities,
             depths,
+            fb_invs,
         })
     }
     /// Returns the total number of reads in this bin.