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@@ -112,7 +112,7 @@ impl Cigar {
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pub struct Alignments {
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pub query_sequence : String,
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pub sam : Vec<Sam>,
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- pub ranges : Vec<Vec<((i32, i32), (i32, i32))>>,
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+ pub ranges : Vec<Vec<((String, i32, i32), (i32, i32))>>,
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}
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impl Alignments {
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@@ -121,7 +121,14 @@ impl Alignments {
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let mut res_ranges = Vec::new();
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for sam in &res_sam {
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- res_ranges.push(ranges_from_cigar(sam.pos, sam.cigar.clone(), sam.is_rc()));
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+ res_ranges.push(
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+ ranges_from_cigar(sam.pos, sam.cigar.clone(), sam.is_rc())
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+ .into_iter()
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+ .map(|(reference, query)| {
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+ ((sam.ref_name.clone(), reference.0, reference.1), query)
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+ })
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+ .collect()
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+ );
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}
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Alignments {
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@@ -130,6 +137,9 @@ impl Alignments {
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ranges: res_ranges
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}
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}
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+ pub fn get_ranges(&self) {
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+
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+ }
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}
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pub fn revcomp(dna: &str) -> String {
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@@ -262,7 +272,7 @@ mod tests {
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let alns = Alignments::to_reference(&sequence, ref_path);
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assert_eq!(
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alns.ranges,
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- vec![vec![((43453321, 43453131), (1, 191))], vec![((22908007, 22908123), (195, 311))]]
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+ vec![vec![(("chr2".to_string(), 43453321, 43453131), (1, 191))], vec![(("chr14".to_string(), 22908007, 22908123), (195, 311))]]
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);
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}
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#[test]
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@@ -283,7 +293,7 @@ mod tests {
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assert_eq!(
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alns.ranges,
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- vec![vec![((22908232, 22908007), (1, 226))], vec![((43453131, 43453227), (230, 326))]]
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+ vec![vec![(("chr14".to_string(), 22908232, 22908007), (1, 226))], vec![(("chr2".to_string(), 43453131, 43453227), (230, 326))]]
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);
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}
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}
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