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@@ -722,7 +722,8 @@ pub fn par_whole_scan(id: &str, time_point: &str, config: &Config) -> anyhow::Re
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bin_size,
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chunk_n_bin,
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config.bam_min_mapq,
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- )?;
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+ )
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+ .with_context(|| format!("failed scanning contig {contig}"))?;
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debug!("Scan {contig}, sorting bins");
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bins.par_sort_unstable_by(|a, b| a.start.cmp(&b.start));
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@@ -732,40 +733,47 @@ pub fn par_whole_scan(id: &str, time_point: &str, config: &Config) -> anyhow::Re
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debug!("Scan {contig}, writing file");
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- {
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- let temp_file = tempfile::NamedTempFile::new_in(&config.tmp_dir)
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- .with_context(|| format!("failed to create temp file in {out_dir:?}"))?;
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-
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- let temp_path = temp_file.into_temp_path();
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+ let out_path = std::path::Path::new(&out_file);
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+ let out_parent = out_path
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+ .parent()
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+ .with_context(|| format!("output file has no parent: {out_file}"))?;
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- {
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- let temp_path_str = temp_path
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- .to_str()
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- .with_context(|| format!("temp path not valid UTF-8: {temp_path:?}"))?;
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+ std::fs::create_dir_all(out_parent)
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+ .with_context(|| format!("failed to create output dir: {out_parent:?}"))?;
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- let mut writer = get_gz_writer(temp_path_str, true)
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- .with_context(|| format!("failed to open BGZF file: {temp_path_str}"))?;
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+ let tmp_path = out_parent.join(format!(
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+ ".{}.{}.{}.tmp",
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+ contig,
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+ std::process::id(),
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+ std::thread::current().name().unwrap_or("rayon")
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+ ));
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- for bin in &bins {
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- writeln!(writer, "{}", bin.to_tsv_row()).with_context(|| {
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- format!("failed writing {contig} row to {temp_path_str}")
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- })?;
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- }
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+ let tmp_path_str = tmp_path
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+ .to_str()
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+ .with_context(|| format!("temp path is not valid UTF-8: {tmp_path:?}"))?;
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- writer
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- .flush()
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- .with_context(|| format!("failed flushing BGZF writer: {temp_path_str}"))?;
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+ {
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+ let mut writer = get_gz_writer(tmp_path_str, true)
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+ .with_context(|| format!("failed to open BGZF temp file: {tmp_path_str}"))?;
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- writer
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- .close()
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- .with_context(|| format!("failed closing BGZF writer: {temp_path_str}"))?;
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+ for bin in &bins {
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+ writeln!(writer, "{}", bin.to_tsv_row()).with_context(|| {
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+ format!("failed writing {contig} row to {tmp_path_str}")
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+ })?;
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}
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- temp_path
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- .persist(&out_file)
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- .with_context(|| format!("failed atomic rename to {out_file}"))?;
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+ writer
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+ .flush()
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+ .with_context(|| format!("failed flushing BGZF writer: {tmp_path_str}"))?;
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+
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+ writer.close().with_context(|| {
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+ format!("failed closing/finalizing BGZF writer: {tmp_path_str}")
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+ })?;
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}
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+ std::fs::rename(&tmp_path, &out_file)
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+ .with_context(|| format!("failed atomic rename {tmp_path_str} -> {out_file}"))?;
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+
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Ok(())
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})?;
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