Convert 1D interval set to indexed format

Converts a per-chromosome interval set to indexed format (intervals.dat + intervals.idx) which reduces file descriptor usage.

gintervals.convert_to_indexed(
  set.name = NULL,
  remove.old = FALSE,
  force = FALSE
)

Arguments

set.name

name of interval set to convert

remove.old

if TRUE, removes old per-chromosome files after successful conversion

force

if TRUE, re-converts even if already in indexed format

Value

invisible NULL

Details

The indexed format stores all chromosomes in a single intervals.dat file with an intervals.idx index file. This reduces file descriptor usage from N files (one per chromosome) to just 2 files.

The conversion process:

1. Creates temporary intervals.dat.tmp and intervals.idx.tmp files

2. Concatenates all per-chromosome files into intervals.dat.tmp

3. Builds index with offsets and checksums

4. Atomically renames temporary files to final names

5. Optionally removes old per-chromosome files

The indexed format is 100

See also

gintervals.save, gintervals.load

Examples

if (FALSE) { # \dontrun{
# Convert an interval set
gintervals.convert_to_indexed("my_intervals")

# Convert and remove old files
gintervals.convert_to_indexed("my_intervals", remove.old = TRUE)

# Force re-conversion
gintervals.convert_to_indexed("my_intervals", force = TRUE)
} # }