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.. _summary:
Summary
=======
These tables summarize BEDOPS utilities by option, file inputs and BED column requirements.
=======================================
Set operation and statistical utilities
=======================================
--------------
``bedextract``
--------------
* Efficiently extracts features from BED input.
* BEDOPS :ref:`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 | 1 | 1 | 3 |
| | input.bed`` | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``<query> <reference>`` | Grab elements of ``query`` that overlap elements in reference. Same | 2 | 2 | 3 |
| | 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. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
----------
``bedmap``
----------
* Maps source signals from ``map-file`` onto qualified target regions from ``ref-file``. Calculates an output for every ``ref-file`` element.
* BEDOPS :ref:`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 | 1 | 2 | 3 |
| | ``ref-file`` 's element. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--bases-uniq`` | Reports the number of distinct bases from ``ref-file`` 's element | 1 | 2 | 3 |
| | overlapped by elements in ``map-file``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--bases-uniq-f`` | Reports the fraction of distinct bases from ``ref-file`` 's element | 1 | 2 | 3 |
| | elements in ``map-file``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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`` | 1 | 2 | 5 |
| | divided by the result of ``--mean``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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`` | 1 | 2 | 5 |
| | elements. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--echo-map-size`` | Calculates difference between start and stop coordinates (or size) | 1 | 2 | 3 |
| | of each mapped element. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--echo-overlap-size`` | Calculates size of overlap between each mapped element and its | 1 | 2 | 3 |
| | reference element. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--echo-ref-name`` | Reports the first 3 fields of ``ref-file`` element in | 1 | 2 | 3 |
| | chrom:start-end format. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--echo-ref-size`` | Reports the length of the ``ref-file`` element. | 1 | 2 | 3 |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--faster`` | **(Advanced)** Strong input assumptions are made. Review documents | 1 | 2 | 5 |
| | before use. Compatible with ``--bp-ovr`` and ``--range`` overlap | | | |
| | options only. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--fraction-ref <val>`` | The fraction of the element's size from ``ref-file`` that must | 1 | 2 | 5 |
| | overlap the element in ``map-file``. Expects ``0 < val <= 1``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--fraction-map <val>`` | The fraction of the element's size from ``map-file`` that must | 1 | 2 | 5 |
| | overlap the element in ``ref-file``. Expects ``0 < val <= 1``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--fraction-both <val>`` | Both ``--fraction-ref <val>`` and ``--fraction-map <val>`` must be | 1 | 2 | 5 |
| | true to qualify as overlapping. Expects ``0 < val <= 1``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--fraction-either <val>`` | Both ``--fraction-ref <val>`` and ``--fraction-map <val>`` must be | 1 | 2 | 5 |
| | true to qualify as overlapping. Expects ``0 < val <= 1``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--exact`` | Shorthand for ``--fraction-both 1``. First three fields from | 1 | 2 | 5 |
| | ``map-file`` must be identical to ``ref-file`` element. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--indicator`` | Reports the presence of one or more overlapping elements in | 1 | 2 | 3 |
| | ``map-file`` as a binary value (``0`` or ``1``). | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--kth <val>`` | Reports the value at the *k* th fraction. A generalized median-like | 1 | 2 | 5 |
| | calculation, where ``--kth 0.5`` is the median. (``0 < val <= 1``) | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--mad <mult=1>`` | Reports the 'median absolute deviation' of overlapping elements in | 1 | 2 | 5 |
| | ``map-file``, multiplied by ``<mult>``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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 | 1 | 2 | 5 |
| | overlapping elements in ``map-file``. If no overlapping element | | | |
| | exists, ``NAN`` is reported (unless ``--skip-unmapped`` is used). | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--max-element-rand`` | A randomly-chosed element with the highest score from overlapping | 1 | 2 | 5 |
| | elements in ``map-file``. If no overlapping element exists, ``NAN`` | | | |
| | is reported (unless ``--skip-unmapped`` is used). | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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 | 1 | 2 | 5 |
| | overlapping elements in ``map-file``. If no overlapping element | | | |
| | exists, ``NAN`` is reported (unless ``--skip-unmapped`` is used). | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--min-element-rand`` | A randomly-chosed element with the lowest score from overlapping | 1 | 2 | 5 |
| | elements in ``map-file``. If no overlapping element exists, ``NAN`` | | | |
| | is reported (unless ``--skip-unmapped`` is used). | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--skip-unmapped`` | Omits printing reference elements which do not associate with any | 1 | 2 | 3 |
| | mapped elements. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--stdev`` | Reports the square root of the result of ``--variance``. | 1 | 2 | 5 |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--sum`` | Reports the accumulated value from scores of overlapping elements in | 1 | 2 | 5 |
| | ``map-file``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--sweep-all`` | Reads through entire ``map-file`` dataset to avoid early termination | 1 | 2 | 3 |
| | that may cause SIGPIPE or other I/O errors. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--tmean <low> <hi>`` | Reports the mean score from overlapping elements in ``map-file``, | 1 | 2 | 5 |
| | after ignoring the bottom ``<low>`` and top ``<hi>`` fractions of | | | |
| | those scores. (``0 <= low <= 1``, ``0 <= hi <= 1``, ``low + hi <= | | | |
| | 1``). | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--variance`` | Reports the variance of scores from overlapping elements in | 1 | 2 | 5 |
| | ``map-file``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
----------
``bedops``
----------
* Offers set and multiset operations for files in BED format.
* BEDOPS :ref:`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 | 1 | No imposed limit | 3 |
| | segments. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--chop``, ``-w`` | Breaks up merged regions into fixed-size chunks, optionally anchored | 1 | No imposed limit | 3 |
| | on start coordinates a fixed distance apart. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--difference``, ``-d`` | Reports the intervals found in the first file that are not present | 2 | No imposed limit | 3 |
| | in any other input file. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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 | 2 | No imposed limit | 3 |
| | percentage or number of base pairs, the merged segments from all | | | |
| | other input files. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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 | 1 | No imposed limit | 3 |
| | and adjoining segments. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--not-element-of``, ``-n`` | Reports exactly everything that ``--element-of`` does not, given the | 2 | No imposed limit | 3 |
| | same overlap criterion. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--partition``, ``-p`` | Reports all disjoint intervals from all input files. Overlapping | 1 | No imposed limit | 3 |
| | segments are cut up into pieces at all segment boundaries. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--range L:R`` | Add ``L`` bases to all start coordinates and ``R`` base to end | 1 | No imposed limit | 3 |
| | 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. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--range S`` | Pad input file(s) coordinates symmetrically by ``S`` bases. This is | 1 | No imposed limit | 3 |
| | shorthand for ``--range -S:S``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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. | 1 | No imposed limit | 3 |
| | Duplicates are retained in the output. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
--------------------
``closest-features``
--------------------
* For every element in ``input-file``, find those elements in ``query-file`` nearest to its left and right edges.
* BEDOPS :ref:`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`` | 2 | 2 | 3 |
| | element and the closest elements in ``query-file``. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--ec`` | Error-check all input files (slower). | 2 | 2 | 3 |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--no-overlaps`` | Do not consider elements that overlap. Overlapping elements, | 2 | 2 | 3 |
| | otherwise, have highest precedence. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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 | 2 | 2 | 3 |
| | leftmost closest element. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
=======
Sorting
=======
------------
``sort-bed``
------------
* Sorts input BED file(s) into the order required by other utilities. Loads all input data into memory.
* BEDOPS :ref:`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 :ref:`sort-bed` | 1 | 1000 | 3 |
| | 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. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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 |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
==========================
Compression and extraction
==========================
----------
``starch``
----------
* Lossless compression of any BED file.
* BEDOPS :ref:`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 | 1 | 1 | 3 |
| | favors storage efficiency, while ``--gzip`` favors compression and | | | |
| | extraction time performance. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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 |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
------------
``unstarch``
------------
* Extraction of a ``starch`` archive or attributes.
* BEDOPS :ref:`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>`` | 1 | 1 | NA |
| | (omitting ``<chromosome>`` shows total non-unique base count). | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--bases-uniq <chromosome>`` | Show unique base counts for optional ``<chromosome>`` (omitting | 1 | 1 | NA |
| | ``<chromosome>`` shows total, unique base count). | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``<chromosome>`` | Decompress information for a single ``<chromosome>`` only. | 1 | 1 | NA |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--duplicatesExist`` or | Report if optional ``<chromosome>`` or chromosomes contain duplicate | 1 | 1 | NA |
| ``--duplicatesExistAsString`` | elements as 0/1 numbers or false/true strings | | | |
| with ``<chromosome>`` | | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--elements <chromosome>`` | Show element count for optional ``<chromosome>`` (omitting | 1 | 1 | NA |
| | ``<chromosome>`` shows total element count). | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--elements-max-string-length`` | Show element maximum string length for optional ``<chromosome>`` | 1 | 1 | NA |
| | (omitting ``<chromosome>`` shows maximum string length over all | | | |
| | chromosomes). | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--is-starch`` | Test if the <starch-file> is a valid starch archive, returning 0/1 | 1 | 1 | NA |
| | for a false/true result | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--list`` or ``--list-json`` | Print the metadata for a ``starch`` file, either in tabular form or | 1 | 1 | NA |
| | with JSON formatting. | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--list-chr`` or | List all chromosomes in ``starch`` archive (similar to | 1 | 1 | NA |
| ``--list-chromosomes`` | ``bedextract --list-chr``). | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--nestedsExist`` or | Report if optional ``<chromosome>`` or chromosomes contain nested | 1 | 1 | NA |
| ``--nestedsExistAsString`` | elements as 0/1 numbers or false/true strings | | | |
| with ``<chromosome>`` | | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--note`` | Show descriptive note (if originally added to archive). | 1 | 1 | NA |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--signature`` with | Show SHA-1 signature of specified chromosome (Base64-encoded) | 1 | 1 | NA |
| ``<chromosome>`` | or all signatures if chromosome is not specified. | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--verify-signature`` with | Compare SHA-1 signature of specified chromosome with signature that | 1 | 1 | NA |
| ``<chromosome>`` | is stored in the archive metadata, reporting error is mismatched. | | | |
+------------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
-------------
``starchcat``
-------------
* Merge multiple ``starch`` archive inputs into one ``starch`` archive output.
* BEDOPS :ref:`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 | 1 | No imposed limit | NA |
| | favors storage efficiency, while ``--gzip`` favors compression and | | | |
| | extraction time performance. | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--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 |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
---------------
``starchstrip``
---------------
* Extract or filter a ``starch`` archive by one or more specified chromosome names.
* BEDOPS :ref:`starchstrip <starchstrip>` documentation.
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| option | description | min. file inputs | max. file inputs | min. BED columns |
+===============================+======================================================================+==================+==================+==================+
| (no option) | NA | 1 | No imposed limit | NA |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--include`` or ``--exclude``| Writes output with inclusion or exclusion of specified chromosome | NA | No imposed limit | NA |
| with <chromosomes> | name records (comma-delimited string). | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
.. |--| unicode:: U+2013 .. en dash
.. |---| unicode:: U+2014 .. em dash, trimming surrounding whitespace
:trim:
|
