rduckhts_bam_insert_size_counts: BAM/CRAM Insert-Size Counts

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

BAM/CRAM Insert-Size Counts

Description

Reduces eligible records into sparse orientation and absolute-TLEN counts using Fulcrum Genomics riker 0.4.1 semantics (MIT). Only non-first segments count; QC-fail records are excluded. The unsuffixed wrapper uses the native reducer; the '_sql' wrapper uses the SQL macro. The SQL arm projects binary CIGAR and flag/coordinate columns only; CRAM decoding also requests sequence and tags internally for long-CIGAR restoration. The native arm avoids these fields. For weighted metrics, materialize the counts and call ‘duckhts_insert_size_metrics(’counts_table')' in SQL.

Usage

rduckhts_bam_insert_size_counts(
  con,
  path,
  reference = NULL,
  include_duplicates = FALSE,
  threads = 1,
  decompression_threads = 0,
  scan_mode = c("auto", "indexed", "sequential"),
  index_path = NULL,
  reference_index_path = NULL
)

rduckhts_bam_insert_size_counts_sql(
  con,
  path,
  reference = NULL,
  include_duplicates = FALSE,
  threads = 1,
  decompression_threads = 0,
  scan_mode = c("auto", "sequential"),
  index_path = NULL
)

Arguments

con	DuckDB connection with DuckHTS loaded.
path	BAM or CRAM path.
reference	Reference FASTA for CRAM, or NULL.
include_duplicates	Include duplicate-flagged records.
threads	Workers, from 1 to 8. The SQL wrapper temporarily sets and restores the connection's DuckDB threads setting; the native wrapper uses indexed histogram workers.
decompression_threads	htslib decompression workers per file handle.
scan_mode	SQL: auto or sequential. Native also accepts indexed; its sequential mode uses one histogram worker.
index_path	Optional BAM/CRAM index path.
reference_index_path	Optional reference FASTA index path (native only).

Value

Data frame with pair_orientation, insert_size and read_pairs. Rows are unordered; absent bins are omitted.

Rduckhts documentation built on Oct. 25, 2026, 1:08 a.m.