[med-svn] [bedtools] 01/05: Imported Upstream version 2.20.1
Andreas Tille
tille at debian.org
Fri Jun 6 20:21:03 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch debian/unstable
in repository bedtools.
commit a0d28a5ed99897d9ed19c890e4a4a27265860cd2
Author: Andreas Tille <tille at debian.org>
Date: Fri Jun 6 21:50:11 2014 +0200
Imported Upstream version 2.20.1
---
Makefile | 7 +-
README.md | 4 +-
RELEASE_HISTORY | 7 +
docs/conf.py | 6 +-
RELEASE_HISTORY => docs/content/history.rst | 482 +++++-----
docs/content/installation.rst | 2 +-
docs/content/tools/jaccard.rst | 3 +
docs/content/tools/map.rst | 2 -
docs/content/tools/merge.rst | 169 ++--
docs/content/tools/unionbedg.rst | 28 +-
docs/index.rst | 3 +-
src/intersectFile/intersectFile.cpp | 3 +-
src/jaccard/Jaccard.cpp | 94 ++
src/{mapFile/mapFile.h => jaccard/Jaccard.h} | 38 +-
src/jaccard/Makefile | 29 +-
src/jaccard/jaccard.cpp | 110 ---
src/jaccard/jaccard.h | 70 --
src/jaccard/jaccardMain.cpp | 240 +++--
src/mapFile/mapFile.h | 1 -
src/mapFile/mapMain.cpp | 18 +-
src/mergeBed/Makefile | 35 -
src/mergeBed/mergeBed.cpp | 359 -------
src/mergeBed/mergeBed.h | 72 --
src/mergeBed/mergeMain.cpp | 184 ----
src/mergeFile/Makefile | 46 +
src/mergeFile/mergeFile.cpp | 39 +
src/mergeFile/mergeFile.h | 37 +
src/mergeFile/mergeMain.cpp | 80 ++
src/nekSandbox1/nekSandboxMain.cpp | 6 +-
src/nucBed/nucBed.cpp | 6 +-
src/sampleFile/SampleFile.cpp | 2 +-
src/shuffleBed/shuffleBed.cpp | 51 +-
src/shuffleBed/shuffleBedMain.cpp | 2 -
src/slopBed/slopBed.cpp | 34 +-
src/utils/BamTools/src/api/BamAlignment.h | 2 +-
src/utils/BamTools/src/api/SamHeader.h | 4 +-
.../src/api/internal/io/TcpSocketEngine_p.h | 2 +-
.../src/api/internal/sam/SamHeaderValidator_p.h | 4 +-
src/utils/BinTree/BinTree.cpp | 9 +-
src/utils/BlockedIntervals/BlockedIntervals.cpp | 6 +-
src/utils/Contexts/ContextBase.cpp | 66 +-
src/utils/Contexts/ContextBase.h | 47 +-
src/utils/Contexts/ContextJaccard.cpp | 109 +++
src/utils/Contexts/ContextJaccard.h | 25 +
src/utils/Contexts/ContextMap.cpp | 10 -
src/utils/Contexts/ContextMap.h | 5 -
src/utils/Contexts/ContextMerge.cpp | 176 ++++
src/utils/Contexts/ContextMerge.h | 31 +
src/utils/Contexts/Makefile | 9 +-
.../FileRecordTools/FileReaders/BamFileReader.cpp | 10 +
.../FileRecordTools/FileReaders/BamFileReader.h | 4 +-
.../FileReaders/BufferedStreamMgr.cpp | 30 +-
.../FileRecordTools/FileReaders/InputStreamMgr.cpp | 21 +-
.../FileRecordTools/FileReaders/InputStreamMgr.h | 7 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 6 +-
src/utils/FileRecordTools/FileRecordMergeMgr.cpp | 217 +++++
src/utils/FileRecordTools/FileRecordMergeMgr.h | 58 ++
src/utils/FileRecordTools/FileRecordMgr.cpp | 186 +---
src/utils/FileRecordTools/FileRecordMgr.h | 79 +-
src/utils/FileRecordTools/Makefile | 10 +-
src/utils/FileRecordTools/Records/BamRecord.cpp | 209 ++--
src/utils/FileRecordTools/Records/BamRecord.h | 27 +-
src/utils/FileRecordTools/Records/BlockMgr.cpp | 16 +-
src/utils/FileRecordTools/Records/BlockMgr.h | 3 +
src/utils/FileRecordTools/Records/EmptyRecord.cpp | 34 +
src/utils/FileRecordTools/Records/EmptyRecord.h | 30 +
src/utils/FileRecordTools/Records/Makefile | 12 +-
src/utils/FileRecordTools/Records/Record.h | 5 +-
src/utils/FileRecordTools/Records/RecordMgr.cpp | 24 +
src/utils/FileRecordTools/Records/RecordMgr.h | 1 +
src/utils/FileRecordTools/Records/StrandQueue.cpp | 131 +++
src/utils/FileRecordTools/Records/StrandQueue.h | 47 +
.../FileRecordTools/Records/recordsTar.tar.gz | Bin 54443 -> 0 bytes
src/utils/GenomeFile/NewGenomeFile.cpp | 12 +-
src/utils/KeyListOps/KeyListOps.cpp | 142 ++-
src/utils/KeyListOps/KeyListOps.h | 20 +
src/utils/KeyListOps/KeyListOpsMethods.cpp | 21 +-
src/utils/KeyListOps/KeyListOpsMethods.h | 13 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 10 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 34 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 1 +
src/utils/bedFile/bedFile.cpp | 14 +
src/utils/bedFile/bedFile.h | 4 +
src/utils/fileType/FileRecordTypeChecker.cpp | 56 +-
src/utils/fileType/FileRecordTypeChecker.h | 19 +-
src/utils/fileType/fileType.cpp | 2 +-
src/utils/general/DualQueue.h | 124 ---
src/utils/general/Makefile | 6 +-
src/utils/general/ParseTools.cpp | 34 +-
src/utils/general/ParseTools.h | 4 +-
src/utils/general/QuickString.h | 1 +
src/utils/general/Tokenizer.cpp | 102 ++
src/utils/general/Tokenizer.h | 57 ++
src/utils/version/version_release.txt | 6 +-
test/general/test-general.sh | 204 +++-
test/intersect/dosLineCharWithExtraTab_b.bed | 4 +
test/intersect/dosLineChar_a.bed | 3 +
test/intersect/headerOnly.vcf | 121 +++
test/intersect/new_test-intersect.sh | 104 +-
test/intersect/oneRecordNoNewline.bed | 1 +
test/jaccard/a.bam | Bin 0 -> 1796 bytes
test/jaccard/aMixedStrands.bed | 12 +
test/jaccard/bMixedStrands.bed | 6 +
test/jaccard/e.bed | 1 +
test/jaccard/test-jaccard.sh | 82 +-
test/jaccard/three_blocks_match.bam | Bin 0 -> 1804 bytes
test/jaccard/three_blocks_match.bed | 1 +
test/map/d.bed | 2 +
test/map/fullFields.bam | Bin 0 -> 25813 bytes
test/map/test-map.sh | 44 +-
test/merge/a.full.bam | Bin 0 -> 1836 bytes
test/merge/a.gff | 6 +
test/merge/b.bed | 7 +
test/merge/bamCol10Collapse.txt | 112 +++
test/merge/bamCol11Collapse.txt | 112 +++
test/merge/bamCol1Collapse.txt | 112 +++
test/merge/bamCol3Collapse.txt | 112 +++
test/merge/bamCol4Mean.txt | 112 +++
test/merge/bamCol5Mean.txt | 112 +++
test/merge/bamCol6Collapse.txt | 112 +++
test/merge/bamCol7Collapse.txt | 112 +++
test/merge/bamCol8Mean.txt | 112 +++
test/merge/bamCol9Mean.txt | 112 +++
test/merge/fullFields.bam | Bin 0 -> 25813 bytes
test/merge/mergeBugTest.bed | 12 +
test/merge/mixedStrands.bed | 12 +
test/merge/precisionTest.bed | 10 +
test/merge/test-merge.sh | 391 ++++++--
test/merge/testA.vcf | 129 +++
test/merge/unsorted.bed | 7 +
test/sample/test-sample.sh | 11 +-
test/shuffle/excl.bed | 9 +
test/shuffle/incl.bed | 9 +
test/shuffle/simrep.bed | 1000 ++++++++++++++++++++
test/shuffle/test-shuffle.sh | 127 +++
test/slop/test-slop.sh | 21 +
test/test.sh | 3 +
137 files changed, 5966 insertions(+), 2116 deletions(-)
diff --git a/Makefile b/Makefile
index 2676748..bbbc437 100644
--- a/Makefile
+++ b/Makefile
@@ -19,12 +19,11 @@ export CXX = g++
#ifeq ($(DEBUG),1)
#export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
#else
-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
+export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDE)
#endif
export LIBS = -lz
export BT_ROOT = src/utils/BamTools/
-
SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/bamToBed \
$(SRC_DIR)/bamToFastq \
@@ -47,7 +46,7 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/linksBed \
$(SRC_DIR)/maskFastaFromBed \
$(SRC_DIR)/mapFile \
- $(SRC_DIR)/mergeBed \
+ $(SRC_DIR)/mergeFile \
$(SRC_DIR)/multiBamCov \
$(SRC_DIR)/multiIntersectBed \
$(SRC_DIR)/nekSandbox1 \
@@ -138,7 +137,7 @@ clean:
.PHONY: clean
test: all
- @cd test; sh test.sh
+ @cd test; bash test.sh
.PHONY: test
diff --git a/README.md b/README.md
index ddef07a..4b65d02 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
bedtools - a swiss army knife for genome arithmetic
===================================================
-**Current version**: 2.19.0
+**Current version**: 2.20.1
Note
-------
@@ -9,6 +9,8 @@ Stable release for bedtools were formerly archived on Google Code. Unfortunately
downloads facility is shutting down; so henceforth, all source code and stable releases will be
maintained via this Github repository.
+**Full documentation**: http://bedtools.readthedocs.org
+
Summary
-------
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
diff --git a/RELEASE_HISTORY b/RELEASE_HISTORY
index b7c34f3..6915470 100644
--- a/RELEASE_HISTORY
+++ b/RELEASE_HISTORY
@@ -1,3 +1,10 @@
+Version 2.18.2 (16-Dec-2013)
+
+bedtools. The changes to bedtools reflect fixes to compilation errors, performance enhancements for smaller files, and a bug fix for BAM files that lack a formal header. Our current focus for the 2.19.* release is is on addressing some standing bug/enhancements and also in updating some of the other more widely used tools (e.g., coverage, map, and substract) to use the new API. We will also continue to look into ways to improve performance while hopefully reducing memory usage for algori [...]
+
+pybedtools. Ryan Dale has updated pybedtools to accomodate bedtools 2.18.*, added unit tests, and provided new functionality and bug fixes. The details for this release are here:
+http://pythonhosted.org/pybedtools/changes.html
+
Version 2.18.1 (16-Dec-2013)
Fixes that address compilation errors with CLANG and force compilation of custom BamTools library.
diff --git a/docs/conf.py b/docs/conf.py
index f5c2ebf..789f221 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -44,16 +44,16 @@ master_doc = 'index'
# General information about the project.
project = u'bedtools'
-copyright = u'2009 - 2013, Aaron R. Quinlan'
+copyright = u'2009 - 2014, Aaron R. Quinlan & Neil Kindlon'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
-version = '2.19.0'
+version = '2.20.1'
# The full version, including alpha/beta/rc tags.
-release = '2.19.0'
+release = '2.20.1'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff --git a/RELEASE_HISTORY b/docs/content/history.rst
similarity index 73%
copy from RELEASE_HISTORY
copy to docs/content/history.rst
index b7c34f3..fdb6664 100644
--- a/RELEASE_HISTORY
+++ b/docs/content/history.rst
@@ -1,9 +1,83 @@
+###############
+Release History
+###############
+
+Version 2.20.1 (23-May-2014)
+============================
+1. Fixed a float rounding bug causing occassional off-by-one issues in the slop added by the ``slop`` tool. Thanks to @slw287r.
+2. Fixed a bug injected in 2.19 arising when files have a single line not ending in a newline. Thanks to @cwarden45.
+
+
+Version 2.20.0 (22-May-2014)
+============================
+
+1. The ``merge`` tool now supports BAM input.
+ - The ``-n``, ``-nms``, and ``-scores`` options are deprecated in favor of the new, substantially more flexible, ``-c`` and ``-o`` options. See the `docs <http://bedtools.readthedocs.org/en/latest/content/tools/merge.html>`_.
+ - It now supports the ``-header`` option.
+ - It now supports the ``-S`` option.
+2. The ``map`` tool now supports BAM input.
+3. The ``jaccard`` tool is now ~3 times faster.
+ - It now supports the ``-split`` option.
+ - It now supports the ``-s`` option.
+ - It now supports the ``-S`` option.
+4. We have fixed several CLANG compiler issues/ Thanks to John Marshall for the thorough report.
+5. We added support for "X" and "=" CIGAR operators. Thanks to Pierre Lindenbaum.
+6. Fixed bugs for empty files.
+7. Improved the ``-incl`` option in the ``shuffle`` tool such that the distibution is much more random.
+8. Fixed a bug in ``slop`` when very large slop values are used.
+
+
+Version 2.19.1 (6-Mar-2014)
+===========================
+
+1. Bug fix to intersect causing BAM footers to be erroneously written when -b is BAM
+2. Speedup for the map tool.
+ - http://bedtools.readthedocs.org/en/latest/_images/map-speed-comparo.png
+3. Map tool now allows multiple columns and operations in a single run.
+ - http://bedtools.readthedocs.org/en/latest/content/tools/map.html#multiple-operations-and-columns-at-the-same-time
+
+
+Version 2.19.0 (8-Feb-2014)
+===========================
+Bug Fixes
+---------
+1. Fixed a long standing bug in which the number of base pairs of overlap was incorrectly calculated when using the -wo option with the -split option. Thanks to many for reporting this.
+2. Fixed a bug in which certain flavors of unmapped BAM alignments were incorrectly rejected in the latest 2.18.* series. Thanks very much to Gabriel Pratt.
+
+Enhancements
+------------
+1. Substantially reduced memory usage, especially when dealing with unsorted data. Memory usage ballooned in the 2.18.* series owing to default buffer sizes we were using in a custom string class. We have adjusted this and the memory usage has returned to 2.17.* levels while maintaining speed increases. Thanks so much to Ian Sudberry rightfully complaining about this!
+
+New features
+------------
+
+1. The latest version of the "map" function is ~3X faster than the one available in version 2.17 and 2.18
+2. The map function now supports the "-split" option, as well as "absmin" and "absmax" operations.
+3. In addition, it supports multiple chromosome sorting criterion by supplying a genome file that defines the expected chromosome order. Here is an example of how to run map with datasets having chromosomes sorted in "version" order, as opposed to the lexicographical chrom order that is the norm.
+
+
+Version 2.18.2 (8-Jan-2014)
+===========================
+
+bedtools
+---------
+The changes to bedtools reflect fixes to compilation errors, performance enhancements for smaller files, and a bug fix for BAM files that lack a formal header. Our current focus for the 2.19.* release is is on addressing some standing bug/enhancements and also in updating some of the other more widely used tools (e.g., coverage, map, and substract) to use the new API. We will also continue to look into ways to improve performance while hopefully reducing memory usage for algorithms that [...]
+
+pybedtools
+----------
+Ryan Dale has updated pybedtools to accomodate bedtools 2.18.*, added unit tests, and provided new functionality and bug fixes. The details for this release are here:
+http://pythonhosted.org/pybedtools/changes.html
+
+
+
Version 2.18.1 (16-Dec-2013)
+============================
Fixes that address compilation errors with CLANG and force compilation of custom BamTools library.
Version 2.18.0 (13-Dec-2013)
+============================
The Google Code site is deprecated
----------------------------------
@@ -23,12 +97,7 @@ Improved performance
The 2.18.0 release leverages these improvements in the "intersect" tool. Forthcoming releases will see the new API applied to other tools, but we started with intersect as it is the most widely used tool in the suite.
-**Performance with sorted datasets.** The "chromsweep" algorithm we use for detecting intersections is now **60 times
-faster** than when it was first release in version 2.16.2, and is **** than the 2.17 release. This makes the
-algorithm slightly faster
-that the algorithm used in the bedops ``bedmap`` tool. As an example, the following [figure](https://dl.dropboxusercontent.com/u/515640/bedtools-intersect-sorteddata.png) demonstrates the speed
-when intersecting GENCODE exons against 1, 10, and 100 million BAM alignments from an exome capture experiment.
-Whereas in version 2.16.2 this wuld have taken 80 minutes, **it now takes 80 seconds**.
+Performance with sorted datasets. The "chromsweep" algorithm we use for detecting intersections is now **60 times faster** than when it was first release in version 2.16.2, and is 15 times than the 2.17 release. This makes the algorithm slightly faster that the algorithm used in the bedops ``bedmap`` tool. As an example, the following [figure](https://dl.dropboxusercontent.com/u/515640/bedtools-intersect-sorteddata.png) demonstrates the speed when intersecting GENCODE exons against 1, 10 [...]
**Greater flexibility.** In addition, BAM, BED, GFF/GTF, or VCF files are now automatically detected whether they are a file, stream, or FIFO in either compressed or uncompressed form. As such, one now longer has specify `-abam` when using BAM input as the "A" file with ``intersect``. Moreover, any file type can be used for either the A or
the B file.
@@ -62,23 +131,29 @@ VCF, and GFF/GTF files.
Enhancements
------------
1. Improvements in the consistency of the output of the ``merge`` tool. Thanks to @kcha.
+
2. A new ``-allowBeyondChromEnd`` option in the ``shuffle`` tool. Thanks to @stephenturner.
[docs](http://bedtools.readthedocs.org/en/latest/content/tools/shuffle.html#allowbeyondchromend-allow-records-to-extend-beyond-the-chrom-length)
+
3. A new ``-noOverlapping`` option that prevents shuffled intervals from overlapping one another. Thanks to @brentp. [docs](http://bedtools.readthedocs.org/en/latest/content/tools/shuffle.html#nooverlapping-prevent-shuffled-intervals-from-overlapping)
+
4. Allow the user to specify the maximum number of shuffling attempts via the ``-maxTries`` option in the ``shuffle`` tool.
-4. Various improvements to the documentation provided by manu different users. Thanks to all.
-5. Added the number of intersections (``n_intersections``) to the Jaccard output. Thanks to @brentp.
-6. Various improvements to the ``tag`` tool.
-7. Added the ``-N`` (remove any) option to the ``subtract`` tool.
+
+5. Various improvements to the documentation provided by manu different users. Thanks to all.
+
+6. Added the number of intersections (``n_intersections``) to the Jaccard output. Thanks to @brentp.
+7. Various improvements to the ``tag`` tool.
+
+8. Added the ``-N`` (remove any) option to the ``subtract`` tool.
Version 2.17.0 (3-Nov-2012)
-=====================
-=== New Tool ===
-=====================
+===========================
+New tools
+---------
We have added a new tool (bedtools "jaccard") for measuring the Jaccard statistic
between two interval files. The Jaccard stat measures the ratio of the length
of the intersection over the length of the union of the two sets. In this
@@ -91,50 +166,33 @@ For more details, see see PMID: 22693437.
We anticipate releasing other statistical measures in forthcoming releases.
-
-
-===================================
-=== New Features & enhancements ===
-===================================
+New Features & enhancements
+---------------------------
1. The genome file drives the BAM header in "bedtools bedtobam"
-
2. Substantially improvement the performance of the -sorted option in
"bedtools intersect" and "bedtools map". For many applications,
bedtools is now nearly as fast as the BEDOPS suite when intersecting
pre-sorted data. This improvement is thanks to Neil Kindlon, a staff
scientist in the Quinlan lab.
-
3. Tightened the logic for handling split (blocked) BAM and BED records
-
4. Added ranged column selection to "bedtools groupby". Thanks to Brent Pedersen"
- e.g., formerly "bedtools groupby -g 1,2,3,4,5"; now "-g 1-5"
-
5. "bedtools getfasta" now properly extracts sequences based on blocked (BED12)
records (e.g., exons from genes in BED12 format).
-
6. "bedtools groupby" now allows a header line in the input.
-
7. With -N, the user can now force the closest interval to have a different name
field in "bedtools closest"
-
8. With -A, the user can now force the subtraction of entire interval when
- any overlap exists in "bedtools subtract".
-
+ any overlap exists in "bedtools subtract".
9. "bedtools shuffle" can now shuffle BEDPE records.
-
10. Improved random number generation.
-
11. Added -split, -s, -S, -f, -r options to "bedtools multicov"
-
12. Improvements to the regression testing framework.
-
13. Standardized the tag reporting logic in "bedtools bamtobed"
-
14. Improved the auto-detection of VCF format. Thanks to Michael James Clark.
-====================
-=== Bug fixes ===
-====================
+Bug fixes
+--------------------
1. Fixed a bug in bedtobam's -bed12 mode.
2. Properly include unaligned BAM alignments with "bedtools intersect"'s -v option.
@@ -146,9 +204,7 @@ We anticipate releasing other statistical measures in forthcoming releases.
5. Corrected missing tab in "bedtools annotate"'s header.
6. Allow int or uint tags in "bedtools bamtobed"
-
-7. "bedtools flank" no longer attempts to take flanks prior to the start of a
- chromosome.
+7. "bedtools flank" no longer attempts to take flanks prior to the start of a chromosome.
8. Eliminated an extraneous tab from "bedtools window" -c.
@@ -159,97 +215,106 @@ We anticipate releasing other statistical measures in forthcoming releases.
Version 2.14.1-3 (2-Nov-2011)
-
+=============================
Bug Fixes
-=========
+---------
1. Corrected the help for closestBed. It now correctly reads -io instead of -no.
2. Fixed regression in closestBed injected in version 2.13.4 whereby B features to the right of an A feature were missed.
-New tool.
-============
+New tool
+---------
1. Added the multiIntersectBed tool for reporting common intervals among multiple **sorted** BED/GFF/VCF files.
Version 2.13.4 (26-Oct-2011)
+============================
Bug Fixes
-=========
+---------
1. The -sorted option (chromsweep) in intersectBed now obeys -s and -S. I had neglected to implement that. Thanks to Paul Ryvkin for pointing this out.
2. The -split option was mistakenly splitting of D CIGAR ops.
3. The Makefile was not including zlib properly for newer versions of GCC. Thanks to Istvan Albert for pointing this out and providing the solution.
Improvements
-============
+------------
1. Thanks to Jacob Biesinger for a new option (-D) in closestBed that will report _signed_ distances. Moreover, the new option allows fine control over whether the distances are reported based on the reference genome or based on the strand of the A or B feature. Many thanks to Jacob.
2. Thanks to some nice analysis from Paul Ryvkin, I realized that the -sorted option was using way too much memory in certain cases where there is a chromosome change in a sorted BED file. This has been corrected.
+
+
Version 2.13.3 (30-Sept-2011)
+=============================
Bug Fixes
-============
+---------
1. intersectBed detected, but did not report overlaps when using BAM input and -bed.
Other
-=====
+-----
1. Warning that -sorted trusts, but does not enforce that data is actually sorted.
Version 2.13.2 (23-Sept-2011)
+=============================
New algorithm
-=============
+-------------
1. Preliminary release of the chrom_sweep algorithm.
New options
-===========
+-----------
1. genomeCoverageBed no longer requires a genome file when working with BAM input. It instead uses the BAM header.
2. tagBam now has a -score option for annotating alignments with the BED "scores" field in annotation files. This overrides the default behavior, which is to use the -labels associated with the annotation files passed in on the command line.
Bug fixes
-=========
+---------
1. Correct a bug that prevented proper BAM support in intersectBed.
2. Improved detection of GFF features with negative coordinates.
Version 2.13.1 (6-Sept-2011)
-
+============================
New options
-===========
+-----------
1. tagBam now has -s and -S options for only annotating alignments with features on the same and opposite strand, respectively.
2. tagBam now has a -names option for annotating alignments with the "name" field in annotation files. This overrides the default behavior, which is to use the -labels associated with the annotation files passed in on the command line. Currently, this works well with BED files, but given the limited metadata support for GFF files, annotating with -names and GFF files may not work as well as wished, depending on the type of GFF file used.
Version 2.13.0 (1-Sept-2011)
+============================
New tools
-=========
+---------
1. tagBam. This tool annotates a BAM file with custom tag fields based on overlaps with BED/GFF/VCF files.
For example:
-$ tagBam -i aln.bam -files exons.bed introns.bed cpg.bed utrs.bed \
- -tags exonic intonic cpg utr \
- > aln.tagged.bam
-For alignments that have overlaps, you should see new BAM tags like "YB:Z:exonic", "YB:Z:cpg;utr"
+::
+
+ $ tagBam -i aln.bam -files exons.bed introns.bed cpg.bed utrs.bed \
+ -tags exonic intonic cpg utr \
+ > aln.tagged.bam
+
+For alignments that have overlaps, you should see new BAM tags like "YB:Z:exonic", "YB:Z:cpg;utr"
2. multiBamCov. The new tool counts sequence coverage for multiple bams at specific loci defined in a BED/GFF/VCF file.
For example:
-$ multiBamCov -bams aln.1.bam aln.2.bam aln3.bam -bed exons.bed
-chr1 861306 861409 SAMD11 1 + 181 280 236
-chr1 865533 865718 SAMD11 2 + 249 365 374
-chr1 866393 866496 SAMD11 3 + 162 298 322
+ $ multiBamCov -bams aln.1.bam aln.2.bam aln3.bam -bed exons.bed
+ chr1 861306 861409 SAMD11 1 + 181 280 236
+ chr1 865533 865718 SAMD11 2 + 249 365 374
+ chr1 866393 866496 SAMD11 3 + 162 298 322
where the last 3 columns represent the number of alignments overlapping each interval from the three BAM file.
The following options are available to control which types of alignments are are counted.
--q Minimum mapping quality allowed. Default is 0.
+ -q Minimum mapping quality allowed. Default is 0.
--D Include duplicate-marked reads. Default is to count non-duplicates only
+ -D Include duplicate-marked reads. Default is to count non-duplicates only
--F Include failed-QC reads. Default is to count pass-QC reads only
+ -F Include failed-QC reads. Default is to count pass-QC reads only
--p Only count proper pairs. Default is to count all alignments with MAPQ
- greater than the -q argument, regardless of the BAM FLAG field.
+ -p Only count proper pairs. Default is to count all alignments with MAPQ
+ greater than the -q argument, regardless of the BAM FLAG field.
3. nucBed. This new tool profiles the nucleotide content of intervals in a fasta file. The following information will be reported after each original BED/GFF/VCF entry:
1) %AT content
@@ -264,47 +329,39 @@ The following options are available to control which types of alignments are are
10) The sequence extracted from the FASTA file. (optional, if -seq is used)
11) The number of times a user defined pattern was observed. (optional, if -pattern is used.)
-
-
For example:
-$ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed | head -3
-#1_usercol 2_usercol 3_usercol 4_usercol 5_usercol 6_usercol 7_pct_at 8_pct_gc 9_num_A 10_num_C 11_num_G 12_num_T 13_num_N 14_num_oth 15_seq_len
-chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468
-chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173
+ $ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed | head -3
+ #1_usercol 2_usercol 3_usercol 4_usercol 5_usercol 6_usercol 7_pct_at 8_pct_gc 9_num_A 10_num_C 11_num_G 12_num_T 13_num_N 14_num_oth 15_seq_len
+ chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468
+ chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173
One can also report the sequence itself:
-$ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed -seq | head -3
-#1_usercol 2_usercol 3_usercol 4_usercol 5_usercol 6_usercol 7_pct_at 8_pct_gc 9_num_A 10_num_C 11_num_G 12_num_T 13_num_N 14_num_oth 15_seq_len 16_seq
-chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468 ccagggg...
-chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173 TCTTTCA...
+ $ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed -seq | head -3
+ #1_usercol 2_usercol 3_usercol 4_usercol 5_usercol 6_usercol 7_pct_at 8_pct_gc 9_num_A 10_num_C 11_num_G 12_num_T 13_num_N 14_num_oth 15_seq_len 16_seq
+ chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468 ccagggg...
+ chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173 TCTTTCA...
Or, one can count the number of times that a specific pattern occur in the intervals (reported as the last column):
-$ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed -pattern CGTT | head
-#1_usercol 2_usercol 3_usercol 4_usercol 5_usercol 6_usercol 7_pct_at 8_pct_gc 9_num_A 10_num_C 11_num_G 12_num_T 13_num_N 14_num_oth 15_seq_len 16_user_patt_count
-chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468 0
-chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173 0
-chr1 10757 10997 trf 434 + 0.370833 0.629167 49 70 81 40 0 0 240 0
-chr1 11225 11447 trf 273 + 0.463964 0.536036 44 86 33 59 0 0 222 0
-chr1 11271 11448 trf 187 + 0.463277 0.536723 37 69 26 45 0 0 177 0
-chr1 11283 11448 trf 199 + 0.466667 0.533333 37 64 24 40 0 0 165 0
-chr1 19305 19443 trf 242 + 0.282609 0.717391 17 57 42 22 0 0 138 1
-chr1 20828 20863 trf 70 + 0.428571 0.571429 10 7 13 5 0 0 35 0
-chr1 30862 30959 trf 79 + 0.556701 0.443299 35 22 21 19 0 0 97 0
-
-
+ $ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed -pattern CGTT | head
+ #1_usercol 2_usercol 3_usercol 4_usercol 5_usercol 6_usercol 7_pct_at 8_pct_gc 9_num_A 10_num_C 11_num_G 12_num_T 13_num_N 14_num_oth 15_seq_len 16_user_patt_count
+ chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468 0
+ chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173 0
+ chr1 10757 10997 trf 434 + 0.370833 0.629167 49 70 81 40 0 0 240 0
+ chr1 11225 11447 trf 273 + 0.463964 0.536036 44 86 33 59 0 0 222 0
+ chr1 11271 11448 trf 187 + 0.463277 0.536723 37 69 26 45 0 0 177 0
+ chr1 11283 11448 trf 199 + 0.466667 0.533333 37 64 24 40 0 0 165 0
+ chr1 19305 19443 trf 242 + 0.282609 0.717391 17 57 42 22 0 0 138 1
+ chr1 20828 20863 trf 70 + 0.428571 0.571429 10 7 13 5 0 0 35 0
+ chr1 30862 30959 trf 79 + 0.556701 0.443299 35 22 21 19 0 0 97 0
New options
-===========
+-----------
1. Support for named pipes and FIFOs.
2. "-" is now allowable to indicate that data is being sent via stdin.
-
3. Multiple tools. Added new -S option to annotateBed, closestBed, coverageBed, intersectBed, pairToBed, subtractBed, and windowBed (-Sm). This new option does the opposite of the -s option: that is, overlaps are only processed if they are on _opposite_ strands. Thanks to Sol Katzman for the great suggestion. Very useful for certain RNA-seq analyses.
-
4. coverageBed. Added a new -counts option to coverageBed that only reports the count of overlaps, instead of also computing fractions, etc. This is much faster and uses much less memory.
-
5. fastaFromBed. Added a new -full option that uses the full BED entry when naming each output sequence. Also removed the -fo option such that all output is now written to stdout.
-
6. genomeCoverageBed.
- Added new -scale option that allows the coverage values to be scaled by a constant. Useful for normalizing coverage with RPM, RPKM, etc. Thanks to Ryan Dale for the useful suggestion.
- Added new -5, -3, -trackline, -trackopts, and -dz options. Many thanks to Assaf Gordon for these improvements.
@@ -313,50 +370,47 @@ New options
-trackline: Adds a UCSC/Genome-Browser track line definition in the first line of the output.
-trackopts: rites additional track line definition parameters in the first line.
-dz: Report the depth at each genome position with zero-based coordinates, instead of zero-based.
-
7. closestBed. See below, thanks to Brent Pedersen, Assaf Gordon, Ryan Layer and Dan Webster for the helpful discussions.
- - closestBed now reports _all_ features in B that overlap A by default. This allows folks to decide which is the "best" overlapping feature on their own.
-
- 2. closestBed now has a "-io" option that ignores overlapping features. In other words, it will only report the closest, non-overlapping feature.
+ - closestBed now reports _all_ features in B that overlap A by default. This allows folks to decide which is the "best" overlapping feature on their own. closestBed now has a "-io" option that ignores overlapping features. In other words, it will only report the closest, non-overlapping feature.
An example:
- $ cat a.bed
- chr1 10 20
+ $ cat a.bed
+ chr1 10 20
- $ cat b.bed
- chr1 15 16
- chr1 16 40
- chr1 100 1000
- chr1 200 1000
+ $ cat b.bed
+ chr1 15 16
+ chr1 16 40
+ chr1 100 1000
+ chr1 200 1000
- $ bin/closestBed -a a.bed -b b.bed
- chr1 10 20 chr1 15 16
- chr1 10 20 chr1 16 40
+ $ bin/closestBed -a a.bed -b b.bed
+ chr1 10 20 chr1 15 16
+ chr1 10 20 chr1 16 40
- $ bin/closestBed -a a.bed -b b.bed -io
- chr1 10 20 chr1 100 1000
+ $ bin/closestBed -a a.bed -b b.bed -io
+ chr1 10 20 chr1 100 1000
Updates
-=======
+-------
1. Updated to the latest version of BamTools. This allows greater functionality and will facilitate new options and tools in the future.
- -
Bug Fixes
-=========
+---------
1. GFF files cannot have zero-length features.
+
2. Corrected an erroneous check on the start coordinates in VCF files. Thanks to Jan Vogel for the correction.
-3. mergeBed now always reports output in BED format.
-3. Updated the text file Tokenizer function to yield 15% speed improvement.
-4. Various tweaks and improvements.
+3. mergeBed now always reports output in BED format.
+4. Updated the text file Tokenizer function to yield 15% speed improvement.
+5. Various tweaks and improvements.
Version 2.12.0 (April-3-2011)
-
+=============================
New Tool
-========
+---------
1. Added new tool called "flankBed", which allows one to extract solely the flanking regions that are upstream and downstream of a given feature. Unlike slopBed, flankBed does not include the original feature itself. A new feature is created for each flabking region. For example, imagine the following feature:
chr1 100 200
@@ -374,7 +428,7 @@ FlankBed has all of the same features as slopBed.
New Features
-============
+-------------
1. Added new "-scores" feature to mergeBed. This allows one to take the sum, min, max,
mean, median, mode, or antimode of merged feature scores. In addition, one can use the "collapse" operation to get a comma-separated list of the merged scores.
2. mergeBed now tolerates multiple features in a merged block to have the same feature name.
@@ -384,7 +438,7 @@ mean, median, mode, or antimode of merged feature scores. In addition, one can
Bug Fixes
-=========
+---------
1. Thanks to Davide Cittaro, intersectBed and windowBed now properly capture unmapped BAM alignments when using the "-v" option.
2. ClosestBed now properly handles cases where b.end == a.start
3. Thanks to John Marshall, the default constructors are much safer and less buggy.
@@ -395,24 +449,23 @@ Bug Fixes
Version 2.11.2 (January-31-2010)
+================================
Fixed a coordinate reporting bug in coverageBed.
Added "max distance (-d)" argument back to the new implementation of mergeBed.
Version 2.11.0 (January-21-2010)
-
+================================
Enhancements:
-=============
+-------------
1. Support for zero length features (i.e., start = end)
- For example, this allows overlaps to be detected with insertions in the reference genome, as reported by dbSNP.
2. Both 8 and 9 column GFF files are now supported.
3. slopBed can now extend the size of features by a percentage of it's size (-pct) instead of just a fixed number of bases.
4. Two improvements to shuffleBed:
- 3a. A -f (overlapFraction) parameter that defines the maximum overlap that a randomized feature can have with an -excl feature.
- That is, if a chosen locus has more than -f overlap with an -excl feature, a new locus is sought.
- 3b. A new -incl option (thanks to Michael Hoffman and Davide Cittaro) that, defines intervals in which the randomized features should be placed. This is used instead of placing the features randomly in the genome. Note that a genome file is still required so
- that a randomized feature does not go beyond the end of a chromosome.
+ 3a. A -f (overlapFraction) parameter that defines the maximum overlap that a randomized feature can have with an -excl feature. That is, if a chosen locus has more than -f overlap with an -excl feature, a new locus is sought.
+ 3b. A new -incl option (thanks to Michael Hoffman and Davide Cittaro) that, defines intervals in which the randomized features should be placed. This is used instead of placing the features randomly in the genome. Note that a genome file is still required so that a randomized feature does not go beyond the end of a chromosome.
5. bamToBed can now optionally report the CIGAR string as an additional field.
6. pairToPair can now report the entire paired feature from the B file when overlaps are found.
7. complementBed now reports all chromosomes, not just those with features in the BED file.
@@ -421,53 +474,56 @@ Enhancements:
Bug Fixes:
-==========
+------------
1. Fixed the "BamAlignmentSupportData is private" compilation issue.
2. Fixed a bug in windowBed that caused positions to run off the end of a chromosome.
Major Changes:
-==============
+---------------
1. The groupBy command is now part of the filo package (https://github.com/arq5x/filo) and will no longer be distributed with BEDTools.
Version 2.10.0 (September-21-2010)
-==New tools==
+==================================
+New tools
+---------
1. annotateBed. Annotates one BED/VCF/GFF file with the coverage and number of overlaps observed
from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command. For example, the following will annotate the fraction of the variants in variants.bed that are covered by genes, conservaed regions and know variation, respectively.
$ annotateBed -i variants.bed -files genes.bed conserv.bed known_var.bed
This tool was suggested by Can Alkan and was motivated by the example source code that he kindly provided.
-==New features==
+New features
+------------
1. New frequency operations (freqasc and freqdesc) added to groupBy. These operations report a histogram of the frequency that each value is observed in a given column.
+
2. Support for writing uncompressed bam with the -ubam option.
+
3. Shorthand arguments for groupBy (-g eq. -grp, -c eq. -opCols, -o eq. -opCols).
-4. In addition, all BEDTools that require only one main input file (the -i file) will assume that input is
-coming from standard input if the -i parameter is ignored. For example, the following are equivalent:
-$ cat snps.bed | sortBed –i stdin
-$ cat snps.bed | sortBed
-As are these:
-$ cat data.txt | groupBy -i stdin -g 1,2,3 -c 5 -o mean
-$ cat data.txt | groupBy -g 1,2,3 -c 5 -o mean
+4. In addition, all BEDTools that require only one main input file (the -i file) will assume that input is coming from standard input if the -i parameter is ignored.
-==Bug fixes==
+Bug fixes
+---------
1. Increased the precision of the output from groupBy.
Version 2.9.0 (August-16-2010)
-==New tools==
+==================================
+New tools
+----------
1. unionBedGraphs. This is a very powerful new tool contributed by Assaf Gordon from CSHL. It will combine/merge multiple BEDGRAPH files into a single file, thus allowing comparisons of coverage (or any text-value) across multiple samples.
-==New features==
+New features
+-------------
1. New "distance feature" (-d) added to closestBed by Erik Arner. In addition to finding the closest feature to each feature in A, the -d option will report the distance to the closest feature in B. Overlapping features have a distance of 0.
2. New "per base depth feature" (-d) added to coverageBed. This reports the per base coverage (1-based) of each feature in file B based on the coverage of features found in file A. For example, this could report the per-base depth of sequencing reads (-a) across each capture target (-b).
-
-==Bug Fixes==
+Bug Fixes
+---------
1. Fixed bug in closestBed preventing closest features from being found for A features with start coordinates < 2048000. Thanks to Erik Arner for pointing this out.
2. Fixed minor reporting annoyances in closestBed. Thanks to Erik Arner.
3. Fixed typo/bug in genomeCoverageBed that reported negative coverage owing to numeric overflow. Thanks to Alexander Dobin for the detailed bug report.
@@ -477,12 +533,14 @@ Version 2.9.0 (August-16-2010)
Version 2.8.3 (July-25-2010)
+==================================
1. Fixed bug that caused some GFF files to be misinterpreted as VCF. This prevented the detection of overlaps.
2. Added a new "-tag" option in bamToBed that allows one to choose the _numeric_ tag that will be used to populate the score field. For example, one could populate the score field with the alignment score with "-tag AS".
3. Updated the BamTools API.
Version 2.8.2 (July-18-2010)
+==================================
1. Fixed a bug in bedFile.h preventing GFF strands from being read properly.
2. Fixed a bug in intersectBed that occasionally caused spurious overlaps between BAM alignments and BED features.
3. Fixed bug in intersectBed causing -r to not report the same result when files are swapped.
@@ -493,37 +551,30 @@ Version 2.8.2 (July-18-2010)
Version 2.8.1 (July-05-2010)
+==================================
1. Added bedToIgv.
Version 2.8.0 (July-04-2010)
-
+==================================
1. Proper support for "split" BAM alignments and "blocked" BED (aka BED12) features. By using the "-split" option, intersectBed, coverageBed, genomeCoverageBed, and bamToBed will now correctly compute overlaps/coverage solely for the "split" portions of BAM alignments or the "blocks" of BED12 features such as genes.
-
2. Added native support for the 1000 Genome Variant Calling Format (VCF) version 4.0.
-
3. New bed12ToBed6 tool. This tool will convert each block of a BED12 feature into discrete BED6 features.
-
4. Useful new groupBy tool. This is a very useful new tool that mimics the "groupBy" clause in SQL. Given a file or stream that is sorted by the appropriate "grouping columns", groupBy will compute summary statistics on another column in the file or stream. This will work with output from all BEDTools as well as any other tab-delimited file or stream. Example summary operations include: sum, mean, stdev, min, max, etc. Please see the help for the tools for examples. The functional [...]
-
5. Improvements to genomeCoverageBed. Applied several code improvements provided by Gordon Assaf at CSHL. Most notably, beyond the several efficiency and organizational changes he made, he include a "-strand" option which allows one to specify that coverage should only be computed on either the "+" or the "-" strand.
-
6. Fixed a bug in closestBed found by Erik Arner (Riken) which incorrectly reported "null" overlaps for features that did not have a closest feature in the B file.
-
7. Fixed a careless bug in slopBed also found by Erik Arner (Riken) that caused an infinite loop when the "-excl" option was used.
-
8. Reduced memory consumption by ca. 15% and run time by ca. 10% for most tools.
-
9. Several code-cleanliness updates such as templated functions and common tyedefs.
-
10. Tweaked the genome binning approach such that 16kb bins are the most granular.
Version 2.7.1 (May-06-2010)
+==================================
Fixed a typo that caused some compilers to fail on closestBed.
Version 2.7.0 (May-05-2010)
-
+==================================
General:
1. "Gzipped" BED and GFF files are now supported as input by all BEDTools. Such files must end in ".gz".
2. Tools that process BAM alignments now uniformly compute an ungapped alignment end position based on the BAM CIGAR string. Specifically, "M", "D" and "N" operations are observed when computing the end position.
@@ -563,60 +614,63 @@ Acknowledgements:
Version 2.6.1 (Mar-29-2010)
+==================================
1. Fixed a careless command line parsing bug in coverageBed.
Version 2.6.0 (Mar-23-2010)
-***Specific improvements / additions to tools***
-1. intersectBed
- * Added an option (-wo) that reports the number of overlapping bases for each intersection b/w A and B files.
- -- Not sure why this wasn't added sooner; it's obvious.
+==================================
+Specific improvements / additions to tools
+------------------------------------------
+1. intersectBed. Added an option (-wo) that reports the number of overlapping bases for each intersection b/w A and B files. Not sure why this wasn't added sooner; it's obvious.
2. coverageBed
- * native BAM support
- * can now report a histogram (-hist) of coverage for each feature in B. Useful for exome sequencing projects, for example.
- -- thanks for the excellent suggestion from Jose Bras
- * faster
+- native BAM support
+- can now report a histogram (-hist) of coverage for each feature in B. Useful for exome sequencing projects, for example. Thanks for the excellent suggestion from Jose Bras
+- faster
3. genomeCoverageBed
- * native BAM support
- * can now report coverage in BEDGRAPH format (-bg)
- -- thanks for the code and great suggestion from Gordon Assaf, CSHL.
+- native BAM support
+- can now report coverage in BEDGRAPH format (-bg). Thanks for the code and great suggestion from Gordon Assaf, CSHL.
4. bamToBed
- * support for "blocked" BED (aka BED12) format. This facilitates the creation of BED entries for "split" alignments (e.g. RNAseq or SV)
- -- thanks to Ann Loraine, UNCC for test data to support this addition.
+- support for "blocked" BED (aka BED12) format. This facilitates the creation of BED entries for "split" alignments (e.g. RNAseq or SV). Thanks to Ann Loraine, UNCC for test data to support this addition.
5. fastaFromBed
- * added the ability to extract sequences from a FASTA file according to the strand in the BED file. That is, when "-" the extracted sequence is reverse complemented.
- -- thanks to Thomas Doktor, U. of Southern Denmark for the code and suggestion.
+- added the ability to extract sequences from a FASTA file according to the strand in the BED file. That is, when "-" the extracted sequence is reverse complemented. Thanks to Thomas Doktor, U. of Southern Denmark for the code and suggestion.
6. ***NEW*** overlap
- * newly added tool for computing the overlap/distance between features on the same line.
- -- For example:
- $ cat test.out
- chr1 10 20 A chr1 15 25 B
- chr1 10 20 C chr1 25 35 D
+- newly added tool for computing the overlap/distance between features on the same line.For example:
+
+ ::
+
+ $ cat test.out
+ chr1 10 20 A chr1 15 25 B
+ chr1 10 20 C chr1 25 35 D
- $ cat test.out | overlaps -i stdin -cols 2,3,6,7
- chr1 10 20 A chr1 15 25 B 5
- chr1 10 20 C chr1 25 35 D -5
+ $ cat test.out | overlaps -i stdin -cols 2,3,6,7
+ chr1 10 20 A chr1 15 25 B 5
+ chr1 10 20 C chr1 25 35 D -5
-***Bug fixes***
+Bug fixes
+------------------------------------------
1. Fixed a bug in pairToBed when comparing paired-end BAM alignments to BED annotations and using the "notboth" option.
2. Fixed an idiotic bug in intersectBed that occasionally caused segfaults when blank lines existed in BED files.
3. Fixed a minor bug in mergeBed when using the -nms option.
-***General changes***
+General changes
+------------------------------------------
1. Added a proper class for genomeFiles. The code is much cleaner and the tools are less sensitive to minor problems with the formatting of genome files. Per Gordon Assaf's wise suggestion, the tools now support "chromInfo" files directly downloaded from UCSC. Thanks Gordon---I disagreed at first, but you were right.
2. Cleaned up some of the code and made the API a bit more streamlined. Will facilitate future tool development, etc.
Version 2.5.4 (Mar-3-2010)
+==================================
1. Fixed an insidious bug that caused malform BAM output from intersectBed and pairToBed. The previous BAM files worked fine with samtools as BAM input, but when piped in as SAM, there was an extra tab that thwarted conversion from SAM back to BAM. Many thanks to Ivan Gregoretti for reporting this bug. I had never used the BAM output in this way and thus never caught the bug!
Version 2.5.3 (Feb-19-2010)
+==================================
1. Fixed bug to "re-allow" track and "browser" lines.
2. Fixed bug in reporting BEDPE overlaps.
3. Fixed bug when using type "notboth" with BAM files in pairToBed.
@@ -626,71 +680,82 @@ Version 2.5.3 (Feb-19-2010)
Version 2.5.2 (Feb-2-2010)
+==================================
1. The start and end coordinates for BED and BEDPE entries created by bamToBed are now based on the __aligned__ sequence, rather than the original sequence. It's obvious, but I missed it originally...sorry.
2. Added an error message to mergeBed preventing one from using "-n" and "-nms" together.
3. Fixed a bug in pairToBed that caused neither -type "notispan" nor "notospan" to behave as described.
... 10151 lines suppressed ...
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