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Older
Version 2.3.3 (12/17/2009)
Rewrote complementBed to use a slower but much simpler approach. This resolves several bugs with the previous logic.
Version 2.3.2 (11/25/2009)
Fixed a bug in subtractBed that prevent a file from subtracting itself when the following is used:
$ subtractBed -a test.bed -b test.bed
Version 2.3.1 (11/19/2009)
Fixed a typo in closestBed that caused all nearby features to be returned instead of just the closest one.
Version 2.3.0 (11/18/2009)
1. Added four new tools:
- shuffleBed. Randomly permutes the locations of a BED file among a genome. Useful for testing for significant overlap enrichments.
- slopBed. Adds a requested number of base pairs to each end of a BED feature. Constrained by the size of each chromosome.
- maskFastaFromBed. Masks a FASTA file based on BED coordinates. Useful making custom genome files from targeted capture experiment, etc.
- pairToPair. Returns overlaps between two paired-end BED files. This is great for finding structural variants that are private or shared among samples.
2. Increased the speed of intersectBed by nearly 50%.
4. Improved sanity checking for BED entries.
Version 2.2.4 (10/27/2009)
1. Updated the mergeBed documentation to describe the -names option which allows one to report the names of the
features that were merged (separated by semicolons).
Version 2.2.3 (10/23/2009)
1. Changed windowBed to optionally define "left" and "right" windows based on strand. For example by default, -l 100 and -r 500 will
add 100 bases to the left (lower coordinates) of a feature in A when scanning for hits in B and 500 bases to the right (higher coordinates).
However if one chooses the -sw option (windows bases on strandedness), the behavior changes. Assume the above example except that a feature in A
is on the negative strand ("-"). In this case, -l 100, -r 500 and -sw will add 100 bases to the right (higher coordinates) and 500 bases to the left (lower coordinates).
In addition, there is a separate option (-sm) that can optionally force hits in B to only be tracked if they are on the same strand as A.
***NOTE: This replaces the previous -s option and may affect existing pipelines***.
Version 2.2.2 (10/20/2009)
1. Improved the speed of genomeCoverageBed by roughly 100 fold. The memory usage is now less than 2.0 Gb.
Version 2.2.1
1. Fixed a very obvious bug in subtractBed that caused improper behavior when a feature in A was overlapped by more than one feature in B.
Many thanks to folks in the Hannon lab at CSHL for pointing this out.
Version 2.2.0
=== Notable changes in this release ===
1. coverageBed will optionally only count features in BED file A (e.g. sequencing reads) that overlap with
the intervals/windows in BED file B on the same strand. This has been requested several times recently
and facilitates CHiP-Seq and RNA-Seq experiments.
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2. intersectBed can now require a minimum __reciprocal__ overlap between intervals in BED A and BED B. For example,
previously, if one used -f 0.90, it required that a feature in B overlap 90% of the feature in A for the "hit"
to be reported. If one adds the -r (reciprocal) option, the hit must also cover 90% of the feature in B. This helps
to exclude overlaps between say small features in A and large features in B:
A ==========
B **********************************************************
-f 0.50 (Reported), whereas -f 0.50 -r (Not reported)
3. The score field has been changed to be a string. While this deviates from the UCSC definition, it allows one to track
much more meaningful information about a feature/interval. For example, score could now be:
7.31E-05 (a p-value)
0.334577 (mean enrichment)
2:2.2:40:2 (several values encoded in a string)
4. closestBed now, by default, reports __all__ intervals in B that overlap equally with an interval in A. Previously, it
merely reported the first such feature that appeared in B. Here's a cartoon explaining the difference.
**Prior behavior**
A ==============
B.1 ++++++++++++++
B.2 ++++++++++++++
B.3 +++++++++
-----------------------------------------
Result = B.1 ++++++++++++++
**Current behavior**
A ==============
B.1 ++++++++++++++
B.2 ++++++++++++++
B.3 +++++++++
-----------------------------------------
Result = B.1 ++++++++++++++
B.2 ++++++++++++++
Using the -t option, one can also choose to report either the first or the last entry in B in the event of a tie.
5. Several other minor changes to the algorithms have been made to increase speed a bit.
VERSION 2.1.2
1. Fixed yet another bug in the parsing of "track" or "browser" lines. Sigh...
2. Change the "score" column (i.e. column 5) to b stored as a string. While this deviates
from the UCSC convention, it allows significantly more information to be packed into the column.
VERSION 2.1.1
1. Added limits.h to bedFile.h to fix compilation issues on some systems.
VERSION 2.1.0
1. Fixed a bug in peIntersectBed that prevented -a from being correctly handled when passed via stdin.
2. Added new functionality to coverageBed that calculates the density of coverage.
3. Fixed bug in geneomCoverageBed.
VERSION 2.0.1
1. Added the ability to retain UCSC browser track/browser headers in BED files.
VERSION 2.0
1. Sped up the file parsing. ~10-20% increase in speed.
2. Created reportBed() as a common method in the bedFile class. Cleans up the code quite nicely.
3. Added the ability to compare BED files accounting for strandedness.
4. Paired-end intersect.
5. Fixed bug that prevented overlaps from being reported when the overlap fraction requested is 1.0
VERSION 1.2, 04/27/2009. (1eb06115bdf3c49e75793f764a70c3501bb53f33)
1. Added subtractBed.
A. Fixed bug that prevented "split" overlaps from being reported.
B. Prevented A from being reported if >=1 feature in B completely spans it.
2. Added linksBed.
3. Added the ability to define separate windows for upstream and downstream to windowBed.
VERSION 1.1, 04/23/2009. (b74eb1afddca9b70bfa90ba763d4f2981a56f432)