Struct AsConfig 

pub struct AsConfig<'a> {
    pub input_path: &'a str,
    pub circ_path: &'a str,
    pub bsj_path: Option<&'a str>,
    pub segment_evidence_paths: Vec<&'a str>,
    pub non_bsj_segment_evidence_paths: Vec<&'a str>,
    pub out_prefix: &'a str,
    pub keep_temp_files: bool,
    pub reference: &'a HashMap<String, String>,
    pub annotation: Option<&'a Annotation>,
    pub min_mapq: i32,
    pub progress_log: Option<&'a mut dyn FnMut(&str, &str) -> Result<()>>,
}

Runtime options for the post-Summary circRNA segments phase.

The fields intentionally reuse the existing CIRI-AS-style second-sweep inputs so read recognition can keep its current parity-sensitive logic while the user-facing output is simplified to <prefix>.segments.

Fields

input_path: &'a str

Original queryname-sorted SAM/BAM used by the main CIRI run.

circ_path: &'a str

Final CIRI3-style circRNA result table used as CIRI-AS -C input.

bsj_path: Option<&'a str>

Final mate-level BSJ table written after Summary.

This file contains both priority=1 CIRI3-compatible evidence and priority=0 mate-level evidence. The segments phase uses it only as post-Summary read/mate annotation; it never feeds these rows back into Summary counts or circRNA discovery.

segment_evidence_paths: Vec<&'a str>

Scan1/Scan2 segment-evidence sidecars produced before Summary.

When present, the segments phase reads these compact alignment dumps and filters them by the final .out junction-read assignments. This avoids a second BAM/SAM scan for confirmed BSJ reads while keeping the sidecar out of Summary’s parity-sensitive inputs.

non_bsj_segment_evidence_paths: Vec<&'a str>

Scan2 non-BSJ topology sidecars produced before Summary.

These rows are read-level candidates, not circRNA-level assignments. They can represent backward/outward evidence with no known BSJ, so the final segments phase skips only reads already assigned as BSJ and then rebuilds the supplemental rows from the read chain itself.

out_prefix: &'a str

Output prefix; the current phase writes <prefix>.segments.

keep_temp_files: bool

Keep shard-local intermediate files after successful segments finalize.

The CLI uses this for --debug. Most retained non-BSJ alignments live in temporary shard streams, so deleting them inside this module would make the user-facing debug flag incomplete.

reference: &'a HashMap<String, String>

In-memory reference sequence map loaded by the main CLI.

annotation: Option<&'a Annotation>

Optional exon-boundary annotation used to resolve ambiguous motif offsets.

CIRI-AS v1.2 does not consult annotation during index_compare, so Perl falls back to hash iteration order when multiple motif offsets are valid. The Rust sidecar deliberately uses annotation as a deterministic biological tie-break before falling back to the lowest offset.

min_mapq: i32

Minimum mapping quality shared with the main BSJ scan.

Outward reads are weaker circRNA evidence than BSJ/backward reads, so the post-Summary detector uses the same user-facing MAPQ threshold instead of the permissive CIRI-AS sidecar constant used for local coverage.

progress_log: Option<&'a mut dyn FnMut(&str, &str) -> Result<()>>

Optional user-facing progress logger supplied by the CLI.

The segments phase owns an internal BAM progress bar, but several correctness-preserving steps run immediately after that bar completes. Routing status through the caller keeps stdout and <prefix>.log consistent with Scan1/Scan2 without giving this module direct log-file ownership.