7. Summary

These tables summarize BEDOPS utilities by option, file inputs and BED column requirements.

7.1. Set operation and statistical utilities

7.1.1. bedextract

• Efficiently extracts features from BED input.

• BEDOPS bedextract documentation.

option	description	min. file inputs	max. file inputs	min. BED columns
--list-chr	Print every chromosome found in input.bed	1	1	3
<chromosome>	Retrieve all rows for specified chromosome, e.g. bedextract chr8 input.bed	1	1	3
<query> <reference>	Grab elements of query that overlap elements in reference. Same as bedops -e -1 query reference, except that this option fails when query contains fully-nested BED elements. May use - to indicate stdin for reference only.	2	2	3

7.1.2. bedmap

• Maps source signals from map-file onto qualified target regions from ref-file. Calculates an output for every ref-file element.

• BEDOPS bedmap documentation.

option	description	min. file inputs	max. file inputs	min. BED columns
--bases	Reports the total number of bases from map-file that overlap the ref-file ‘s element.	1	2	3
--bases-uniq	Reports the number of distinct bases from ref-file ‘s element overlapped by elements in map-file.	1	2	3
--bases-uniq-f	Reports the fraction of distinct bases from ref-file ‘s element elements in map-file.	1	2	3
--bp-ovr <int>	Require <int> bases of overlap between elements of input files.	1	2	3
--chrom <chromosome>	Process data for given <chromosome> only.	1	2	3
--count	Reports the number of overlapping elements in map-file.	1	2	3
--cv	Reports the Coefficient of Variation: the result of --stdev divided by the result of --mean.	1	2	5
--ec	Error-check all input files (slower).	1	2	3
--echo	Echo each line from ref-file.	1	2	3
--echo-map	Reports the overlapping elements found in map-file.	1	2	3
--echo-map-id	Reports the IDs (4th column) from overlapping map-file elements.	1	2	4
--echo-map-id-uniq	List unique IDs from overlapping map-file elements.	1	2	4
--echo-map-range	Reports the genomic range of overlapping elements from map-file.	1	2	3
--echo-map-score	Reports the scores (5th column) from overlapping map-file elements.	1	2	5
--echo-map-size	Calculates difference between start and stop coordinates (or size) of each mapped element.	1	2	3
--echo-overlap-size	Calculates size of overlap between each mapped element and its reference element.	1	2	3
--echo-ref-name	Reports the first 3 fields of ref-file element in chrom:start-end format.	1	2	3
--echo-ref-size	Reports the length of the ref-file element.	1	2	3
--faster	(Advanced) Strong input assumptions are made. Review documents before use. Compatible with --bp-ovr and --range overlap options only.	1	2	5
--fraction-ref <val>	The fraction of the element’s size from ref-file that must overlap the element in map-file. Expects 0 < val <= 1.	1	2	5
--fraction-map <val>	The fraction of the element’s size from map-file that must overlap the element in ref-file. Expects 0 < val <= 1.	1	2	5
--fraction-both <val>	Both --fraction-ref <val> and --fraction-map <val> must be true to qualify as overlapping. Expects 0 < val <= 1.	1	2	5
--fraction-either <val>	Both --fraction-ref <val> and --fraction-map <val> must be true to qualify as overlapping. Expects 0 < val <= 1.	1	2	5
--exact	Shorthand for --fraction-both 1. First three fields from map-file must be identical to ref-file element.	1	2	5
--indicator	Reports the presence of one or more overlapping elements in map-file as a binary value (0 or 1).	1	2	3
--kth <val>	Reports the value at the k th fraction. A generalized median-like calculation, where --kth 0.5 is the median. (0 < val <= 1)	1	2	5
--mad <mult=1>	Reports the ‘median absolute deviation’ of overlapping elements in map-file, multiplied by <mult>.	1	2	5
--max	Reports the highest score from overlapping elements in map-file.	1	2	5
--max-element	The lexicographically “smallest” element with the highest score from overlapping elements in map-file. If no overlapping element exists, NAN is reported (unless --skip-unmapped is used).	1	2	5
--max-element-rand	A randomly-chosed element with the highest score from overlapping elements in map-file. If no overlapping element exists, NAN is reported (unless --skip-unmapped is used).	1	2	5
--mean	Reports the average score from overlapping elements in map-file.	1	2	5
--median	Reports the median score from overlapping elements in map-file.	1	2	5
--min	Reports the lowest score from overlapping elements in map-file.	1	2	5
--min-element	The lexicographically “smallest” element with the lowest score from overlapping elements in map-file. If no overlapping element exists, NAN is reported (unless --skip-unmapped is used).	1	2	5
--min-element-rand	A randomly-chosed element with the lowest score from overlapping elements in map-file. If no overlapping element exists, NAN is reported (unless --skip-unmapped is used).	1	2	5
--skip-unmapped	Omits printing reference elements which do not associate with any mapped elements.	1	2	3
--stdev	Reports the square root of the result of --variance.	1	2	5
--sum	Reports the accumulated value from scores of overlapping elements in map-file.	1	2	5
--sweep-all	Reads through entire map-file dataset to avoid early termination that may cause SIGPIPE or other I/O errors.	1	2	3
--tmean <low> <hi>	Reports the mean score from overlapping elements in map-file, after ignoring the bottom <low> and top <hi> fractions of those scores. (0 <= low <= 1, 0 <= hi <= 1, low + hi <= 1).	1	2	5
--variance	Reports the variance of scores from overlapping elements in map-file.	1	2	5

7.1.3. bedops

• Offers set and multiset operations for files in BED format.

• BEDOPS bedops documentation.

option	description	min. file inputs	max. file inputs	min. BED columns
--chrom <chromosome>	Process data for given chromosome only.	1	No imposed limit	3
--complement, -c	Reports the intervening intervals between the input coordinate segments.	1	No imposed limit	3
--chop, -w	Breaks up merged regions into fixed-size chunks, optionally anchored on start coordinates a fixed distance apart.	1	No imposed limit	3
--difference, -d	Reports the intervals found in the first file that are not present in any other input file.	2	No imposed limit	3
--ec	Error-check input files (slower).	1	No imposed limit	3
--element-of, -e	Reports rows from the first file that overlap, by a specified percentage or number of base pairs, the merged segments from all other input files.	2	No imposed limit	3
--header	Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.	1	No imposed limit	3
--intersect, -i	Reports the intervals common to all input files.	2	No imposed limit	3
--merge, -m	Reports intervals from all input files, after merging overlapping and adjoining segments.	1	No imposed limit	3
--not-element-of, -n	Reports exactly everything that --element-of does not, given the same overlap criterion.	2	No imposed limit	3
--partition, -p	Reports all disjoint intervals from all input files. Overlapping segments are cut up into pieces at all segment boundaries.	1	No imposed limit	3
--range L:R	Add L bases to all start coordinates and R base to end coordinates. Either value may be positive or negative to grow or shrink regions, respectively. With the -e or -n operation, the first (reference) file is not padded, unlike all other files.	1	No imposed limit	3
--range S	Pad input file(s) coordinates symmetrically by S bases. This is shorthand for --range -S:S.	1	No imposed limit	3
--symmdiff, -s	Reports the intervals found in exactly one input file.	2	No imposed limit	3
--everything, -u	Reports the intervals from all input files in sorted order. Duplicates are retained in the output.	1	No imposed limit	3

7.1.4. closest-features

• For every element in input-file, find those elements in query-file nearest to its left and right edges.

• BEDOPS closest-features documentation.

option	description	min. file inputs	max. file inputs	min. BED columns
(no option)	NA	2	2	3
--chrom <chromosome>	Process data for given <chromosome> only.	2	2	3
--dist	Output includes the signed distances between the input-file element and the closest elements in query-file.	2	2	3
--ec	Error-check all input files (slower).	2	2	3
--no-overlaps	Do not consider elements that overlap. Overlapping elements, otherwise, have highest precedence.	2	2	3
--no-ref	Do not echo elements from input-file.	2	2	3
--closest	Choose the nearest element from query-file only. Ties go to the leftmost closest element.	2	2	3

7.2. Sorting

7.2.1. sort-bed

• Sorts input BED file(s) into the order required by other utilities. Loads all input data into memory.

• BEDOPS sort-bed documentation.

option	description	min. file inputs	max. file inputs	min. BED columns
(no option)	NA	1	1000	3
--max-mem <val>	<val> specifies the maximum memory usage for the sort-bed process, which is useful for very large BED inputs. For example, --max-mem may be 8G, 8000M, or 8000000000 to specify 8 GB of memory.	1	1000	3
--unique	Report unique elements (those which only occur once) in output.	1	1000	3
--duplicates	Report duplicate elements (those which occur 2+ times) in output.	1	1000	3

7.3. Compression and extraction

7.3.1. starch

• Lossless compression of any BED file.

• BEDOPS starch documentation.

option	description	min. file inputs	max. file inputs	min. BED columns
(no option)	NA	1	1	3
--bzip2 or --gzip	The internal compression method. The default --bzip2 method favors storage efficiency, while --gzip favors compression and extraction time performance.	1	1	3
--note="foo bar..."	Append note to output archive metadata (optional).	1	1	3
--report-progress=N	Write progress to standard error stream for every N input elements.	1	1	3

7.3.2. unstarch

• Extraction of a starch archive or attributes.

• BEDOPS unstarch documentation.

option	description	min. file inputs	max. file inputs	min. BED columns
(no option)	NA	1	1	NA
--archive-type	Show archive’s compression type (either bzip2 or gzip).	1	1	NA
--archive-version	Show archive version (at this time, either 1.x or 2.x).	1	1	NA
--archive-timestamp	Show archive creation timestamp (ISO 8601 format).	1	1	NA
--bases <chromosome>	Show total, non-unique base counts for optional <chromosome> (omitting <chromosome> shows total non-unique base count).	1	1	NA
--bases-uniq <chromosome>	Show unique base counts for optional <chromosome> (omitting <chromosome> shows total, unique base count).	1	1	NA
<chromosome>	Decompress information for a single <chromosome> only.	1	1	NA
--duplicatesExist or --duplicatesExistAsString with <chromosome>	Report if optional <chromosome> or chromosomes contain duplicate elements as 0/1 numbers or false/true strings	1	1	NA
--elements <chromosome>	Show element count for optional <chromosome> (omitting <chromosome> shows total element count).	1	1	NA
--elements-max-string-length	Show element maximum string length for optional <chromosome> (omitting <chromosome> shows maximum string length over all chromosomes).	1	1	NA
--is-starch	Test if the <starch-file> is a valid starch archive, returning 0/1 for a false/true result	1	1	NA
--list or --list-json	Print the metadata for a starch file, either in tabular form or with JSON formatting.	1	1	NA
--list-chr or --list-chromosomes	List all chromosomes in starch archive (similar to bedextract --list-chr).	1	1	NA
--nestedsExist or --nestedsExistAsString with <chromosome>	Report if optional <chromosome> or chromosomes contain nested elements as 0/1 numbers or false/true strings	1	1	NA
--note	Show descriptive note (if originally added to archive).	1	1	NA
--signature with <chromosome>	Show SHA-1 signature of specified chromosome (Base64-encoded) or all signatures if chromosome is not specified.	1	1	NA
--verify-signature with <chromosome>	Compare SHA-1 signature of specified chromosome with signature that is stored in the archive metadata, reporting error is mismatched.	1	1	NA

7.3.3. starchcat

• Merge multiple starch archive inputs into one starch archive output.

• BEDOPS starchcat documentation.

option	description	min. file inputs	max. file inputs	min. BED columns
(no option)	NA	1	No imposed limit	NA
--bzip2 or --gzip	The internal compression method. The default --bzip2 method favors storage efficiency, while --gzip favors compression and extraction time performance.	1	No imposed limit	NA
--note="foo bar..."	Append note to output archive metadata (optional).	1	No imposed limit	NA
--report-progress=N	Write progress to standard error stream for every N input elements.	1	No imposed limit	NA

7.3.4. starchstrip

• Extract or filter a starch archive by one or more specified chromosome names.

• BEDOPS starchstrip documentation.

option	description	min. file inputs	max. file inputs	min. BED columns
(no option)	NA	1	No imposed limit	NA
--include or --exclude with <chromosomes>	Writes output with inclusion or exclusion of specified chromosome name records (comma-delimited string).	NA	No imposed limit	NA