Module utils 

Utility module: Common bioinformatics and string processing functions.

This module provides the AlignmentRecord abstraction and helper functions like reverse complementation and memory unit parsing.

Structs

AlignmentRecord

Unified representation of one alignment record used by Scan1 and Scan2.

Constants

MIN_BAM_SHARD_BYTES

Smallest compressed BAM shard size worth parallelizing.

Functions

alignment_short_cs

Builds a minimap2-compatible short-form cs payload for one mapper alignment.

bam_shard_count

Chooses a safe BAM shard count for BGZF-parallel Scan1/Scan2 processing.

bsj1_path_for_output

Returns the merged Scan1 BSJ output path for one CLI prefix.

bsj2_path_for_output

Returns the basename used for Scan2 shard-local BSJ spill files.

bsj_is_summary_priority

Returns whether a BSJ row should participate in the Java-compatible summary.

bsj_path_for_output

Returns the final combined BSJ output path for one CLI prefix.

bsj_payload_start

Returns the first field index of the legacy BSJ payload.

clip_sequence_payload

Encodes only recoverable soft-clipped bases for segment-evidence sidecars.

fsj_path_for_output

Returns the basename used for FSJ shard-local spill files.

is_bsj_mate_label

Returns whether a field is the mate label used by the expanded BSJ protocol.

local_clip_evidence_lines

Adds pseudo-alignment rows for local clip evidence accepted with BSJ calls.

log_path_for_output

Returns the sidecar log path for one CLI prefix.

parse_cigar_ops_basic

Parses a SAM-like CIGAR into (length, op) pairs for sidecar formatting.

parse_mem_str

Parses memory strings like 2G, 512M, or 1024K into bytes.

part_path

Returns the temporary spill-file path for one shard-local intermediate.

perf_path_for_output

Returns the profiling report path for one CLI prefix.

result_path_for_output

Returns the final Summary output path for one CLI -o/--out prefix.

reverse_complement

Returns the reverse complement of a DNA sequence.

segments1_path_for_output

Returns the Scan1 segments-evidence sidecar path for one CLI prefix.

segments2_path_for_output

Returns the Scan2 segments-evidence sidecar path for one CLI prefix.

segments_non_bsj_path_for_output

Returns the Scan2 non-BSJ segments sidecar path for one CLI prefix.

trace_path_for_output

Returns the targeted read-trace path for one CLI prefix.