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@@ -5,7 +5,7 @@ use rust_htslib::bam::{self, Record};
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use uuid::Uuid;
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use std::{
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collections::{HashMap, VecDeque},
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- fmt,
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+ fmt, fs::File, io::BufWriter,
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};
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#[derive(Debug, Clone)]
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@@ -321,6 +321,11 @@ impl Contig {
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.sort_by(|a, b| a.target_start.cmp(&b.target_start));
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}
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+ pub fn to_igv(&mut seld) -> {
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+
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+ }
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+
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+ // bug cigar len != seq len
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pub fn write_bam(&self, path: &str) -> Result<()> {
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let aligner = Aligner::builder()
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.asm5()
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@@ -394,6 +399,15 @@ fn group_mappings(mappings: &mut Vec<Mapping>) -> Result<Vec<Vec<Mapping>>> {
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Ok(alignments)
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}
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+// unique
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+pub fn write_fastq(fastq_path: &str, d: &Vec<Record>) {
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+ let file = File::create(fasta_path).unwrap();
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+ let mut writer = BufWriter::new(file);
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+ for record in d {
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+ seq_io::fastq::write_parts(&mut writer, record.qname(), None, &record.seq().as_bytes(), record.qual());
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+ }
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+}
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+
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#[cfg(test)]
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mod tests {
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use super::*;
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