bed fix off-by-one since noodles uses 1-based

examples/intersect.rs

@@ -87,7 +87,7 @@ fn main() -> io::Result<()> {
             &args.a_requirements,
             &args.b_requirements,
         );
-        eprintln!("{:?} {:?}", report.len(), report);
+        //eprintln!("{:?} {:?}", report.len(), report);
         //eprintln!("a reqs: {:?}", args.a_requirements);
 
         if args.count {
@@ -106,6 +106,22 @@ fn main() -> io::Result<()> {
             )?;
             continue;
         }
+        if args.count_base {
+            writeln!(
+                &mut stdout,
+                "{}\t{}\t{}\t{}",
+                intersection.base_interval.chrom(),
+                intersection.base_interval.start(),
+                intersection.base_interval.stop(),
+                report
+                    .count_bases_by_id()
+                    .iter()
+                    .map(|x| x.to_string())
+                    .collect::<Vec<_>>()
+                    .join(",")
+            )?;
+            continue;
+        }
 
         writeln!(
             &mut stdout,

src/bedder_bed.rs

@@ -22,7 +22,7 @@ impl crate::position::Positioned for bed::record::Record<3> {
 
     fn set_start(&mut self, start: u64) {
         // must build a new record to set start.
-        let pstart = core::Position::try_from(start as usize).expect("invalid start");
+        let pstart = core::Position::try_from(start as usize + 1).expect("invalid start");
         let record = bed::Record::<3>::builder()
             .set_reference_sequence_name(self.reference_sequence_name())
             .set_start_position(pstart)
@@ -33,9 +33,9 @@ impl crate::position::Positioned for bed::record::Record<3> {
         *self = record;
     }
 
-    fn set_stop(&mut self, start: u64) {
+    fn set_stop(&mut self, stop: u64) {
         // must build a new record to set start.
-        let pstop = core::Position::try_from(start as usize + 1).expect("invalid start");
+        let pstop = core::Position::try_from(stop as usize).expect("invalid stop");
         let record = bed::Record::<3>::builder()
             .set_reference_sequence_name(self.reference_sequence_name())
             .set_start_position(self.start_position())

src/report.rs

@@ -45,4 +45,25 @@ impl Report {
         });
         result
     }
+
+    /// The number of b-bases in each fragment from each source(id)
+    /// This is determined by the overlap requirements, modes, and parts.
+    pub fn count_bases_by_id(&self) -> Vec<u64> {
+        let mut result = Vec::new();
+        self.0.iter().for_each(|frag| {
+            eprintln!("frag: {:?}", frag);
+            if frag.id >= result.len() {
+                result.resize(frag.id + 1, 0);
+            }
+            result[frag.id] += frag
+                .b
+                .iter()
+                .map(|pos| {
+                    eprintln!("start: {:?} stop: {:?}", pos.start(), pos.stop());
+                    pos.stop() - pos.start()
+                })
+                .sum::<u64>();
+        });
+        result
+    }
 }