Module stream 

Streaming a FASTA file through the curvature calculation.

Scores are handed to a callback as they are produced and then dropped, so the amount held at once is a batch of chunks rather than a genome. What is not bounded here is the sequence itself: without an index the FASTA reader yields a whole record at a time, so the largest record is a floor on the footprint.

Structs

RunStats

How the scoring run went, for reporting.

ScanConfig

Everything a scoring run needs beyond the input file itself.

Functions

chrom_sizes

Read just the names and lengths of each record.

chrom_sizes_from_index

Chromosome names and lengths straight from an index, with no sequence read at all.

for_each_record_calls

Score every record and hand its nucleosome calls to on_record, with the sequence.

for_each_score

Score every record in input, passing each score to emit as it is produced.

for_each_score_indexed

Score every record, reading each one a window at a time through a FASTA index.

load_index

Read <input>.fai if it is there.

Type Aliases

ChromSize

A chromosome name and its length, as needed for a bigWig header.