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@@ -123,6 +123,33 @@ pub fn get_n_start(
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// Ok(start_positions.len())
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}
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+pub fn get_n_start_end_qual(
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+ bam: &mut rust_htslib::bam::IndexedReader,
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+ chr: &str,
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+ start: i32,
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+ stop: i32,
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+ mapq: u8
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+) -> Result<usize> {
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+ bam.fetch((chr, start, stop))?;
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+
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+ // let mut start_positions = Vec::new();
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+ let mut n_start = 0;
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+ for read in bam.records() {
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+ let record = read.context(format!("eRR"))?;
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+ let rstart = record.pos() as i32;
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+ let rend = record.reference_end() as i32;
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+ if rstart >= start && rstart < stop || rend >= start && rend < stop {
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+ if record.mapq() >= mapq {
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+ n_start += 1;
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+ }
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+ }
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+ }
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+
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+ Ok(n_start)
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+ // Ok(start_positions.len())
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+}
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+
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+
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pub fn range_depths(
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bam: &mut rust_htslib::bam::IndexedReader,
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chr: &str,
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