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comparison BEDTools-Version-2.14.3/RELEASE_HISTORY @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 Version 2.14.2 (2-Nov-2011)
2
3 Bug Fixes
4 =========
5 1. Corrected the help for closestBed. It now correctly reads -io instead of -no.
6 2. Fixed regression in closestBed injected in version 2.13.4 whereby B features to the right of an A feature were missed.
7
8 New tool.
9 ============
10 1. Added the multiIntersectBed tool for reporting common intervals among multiple **sorted** BED/GFF/VCF files.
11
12
13
14 Version 2.13.4 (26-Oct-2011)
15 Bug Fixes
16 =========
17 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.
18 2. The -split option was mistakenly splitting of D CIGAR ops.
19 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.
20
21 Improvements
22 ============
23 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.
24 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.
25
26 Version 2.13.3 (30-Sept-2011)
27 Bug Fixes
28 ============
29 1. intersectBed detected, but did not report overlaps when using BAM input and -bed.
30
31 Other
32 =====
33 1. Warning that -sorted trusts, but does not enforce that data is actually sorted.
34
35
36 Version 2.13.2 (23-Sept-2011)
37
38 New algorithm
39 =============
40 1. Preliminary release of the chrom_sweep algorithm.
41
42 New options
43 ===========
44 1. genomeCoverageBed no longer requires a genome file when working with BAM input. It instead uses the BAM header.
45 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.
46
47 Bug fixes
48 =========
49 1. Correct a bug that prevented proper BAM support in intersectBed.
50 2. Improved detection of GFF features with negative coordinates.
51
52
53
54 Version 2.13.1 (6-Sept-2011)
55
56 New options
57 ===========
58 1. tagBam now has -s and -S options for only annotating alignments with features on the same and opposite strand, respectively.
59 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.
60
61
62
63 Version 2.13.0 (1-Sept-2011)
64
65 New tools
66 =========
67 1. tagBam. This tool annotates a BAM file with custom tag fields based on overlaps with BED/GFF/VCF files.
68 For example:
69 $ tagBam -i aln.bam -files exons.bed introns.bed cpg.bed utrs.bed \
70 -tags exonic intonic cpg utr \
71 > aln.tagged.bam
72 For alignments that have overlaps, you should see new BAM tags like "YB:Z:exonic", "YB:Z:cpg;utr"
73
74 2. multiBamCov. The new tool counts sequence coverage for multiple bams at specific loci defined in a BED/GFF/VCF file.
75 For example:
76
77 $ multiBamCov -bams aln.1.bam aln.2.bam aln3.bam -bed exons.bed
78 chr1 861306 861409 SAMD11 1 + 181 280 236
79 chr1 865533 865718 SAMD11 2 + 249 365 374
80 chr1 866393 866496 SAMD11 3 + 162 298 322
81
82 where the last 3 columns represent the number of alignments overlapping each interval from the three BAM file.
83
84 The following options are available to control which types of alignments are are counted.
85 -q Minimum mapping quality allowed. Default is 0.
86
87 -D Include duplicate-marked reads. Default is to count non-duplicates only
88
89 -F Include failed-QC reads. Default is to count pass-QC reads only
90
91 -p Only count proper pairs. Default is to count all alignments with MAPQ
92 greater than the -q argument, regardless of the BAM FLAG field.
93
94 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:
95 1) %AT content
96 2) %GC content
97 3) Number of As observed
98 4) Number of Cs observed
99 5) Number of Gs observed
100 6) Number of Ts observed
101 7) Number of Ns observed
102 8) Number of other bases observed
103 9) The length of the explored sequence/interval.
104 10) The sequence extracted from the FASTA file. (optional, if -seq is used)
105 11) The number of times a user defined pattern was observed. (optional, if -pattern is used.)
106
107
108
109 For example:
110 $ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed | head -3
111 #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
112 chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468
113 chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173
114
115
116 One can also report the sequence itself:
117 $ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed -seq | head -3
118 #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
119 chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468 ccagggg...
120 chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173 TCTTTCA...
121
122 Or, one can count the number of times that a specific pattern occur in the intervals (reported as the last column):
123 $ nucBed -fi ~/data/genomes/hg18/hg18.fa -bed simrep.bed -pattern CGTT | head
124 #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
125 chr1 10000 10468 trf 789 + 0.540598 0.459402 155 96 119 98 0 0 468 0
126 chr1 10627 10800 trf 346 + 0.445087 0.554913 54 55 41 23 0 0 173 0
127 chr1 10757 10997 trf 434 + 0.370833 0.629167 49 70 81 40 0 0 240 0
128 chr1 11225 11447 trf 273 + 0.463964 0.536036 44 86 33 59 0 0 222 0
129 chr1 11271 11448 trf 187 + 0.463277 0.536723 37 69 26 45 0 0 177 0
130 chr1 11283 11448 trf 199 + 0.466667 0.533333 37 64 24 40 0 0 165 0
131 chr1 19305 19443 trf 242 + 0.282609 0.717391 17 57 42 22 0 0 138 1
132 chr1 20828 20863 trf 70 + 0.428571 0.571429 10 7 13 5 0 0 35 0
133 chr1 30862 30959 trf 79 + 0.556701 0.443299 35 22 21 19 0 0 97 0
134
135
136
137 New options
138 ===========
139 1. Support for named pipes and FIFOs.
140 2. "-" is now allowable to indicate that data is being sent via stdin.
141
142 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.
143
144 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.
145
146 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.
147
148 6. genomeCoverageBed.
149 - 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.
150 - Added new -5, -3, -trackline, -trackopts, and -dz options. Many thanks to Assaf Gordon for these improvements.
151 -5: Calculate coverage of 5" positions (instead of entire interval)
152 -3: Calculate coverage of 3" positions (instead of entire interval).
153 -trackline: Adds a UCSC/Genome-Browser track line definition in the first line of the output.
154 -trackopts: rites additional track line definition parameters in the first line.
155 -dz: Report the depth at each genome position with zero-based coordinates, instead of zero-based.
156
157 7. closestBed. See below, thanks to Brent Pedersen, Assaf Gordon, Ryan Layer and Dan Webster for the helpful discussions.
158 - 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.
159
160 2. closestBed now has a "-io" option that ignores overlapping features. In other words, it will only report the closest, non-overlapping feature.
161
162 An example:
163
164 $ cat a.bed
165 chr1 10 20
166
167 $ cat b.bed
168 chr1 15 16
169 chr1 16 40
170 chr1 100 1000
171 chr1 200 1000
172
173 $ bin/closestBed -a a.bed -b b.bed
174 chr1 10 20 chr1 15 16
175 chr1 10 20 chr1 16 40
176
177 $ bin/closestBed -a a.bed -b b.bed -io
178 chr1 10 20 chr1 100 1000
179
180 Updates
181 =======
182 1. Updated to the latest version of BamTools. This allows greater functionality and will facilitate new options and tools in the future.
183
184 -
185 Bug Fixes
186 =========
187 1. GFF files cannot have zero-length features.
188 2. Corrected an erroneous check on the start coordinates in VCF files. Thanks to Jan Vogel for the correction.
189 3. mergeBed now always reports output in BED format.
190 3. Updated the text file Tokenizer function to yield 15% speed improvement.
191 4. Various tweaks and improvements.
192
193
194
195
196 Version 2.12.0 (April-3-2011)
197
198 New Tool
199 ========
200 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:
201
202 chr1 100 200
203
204 The following would create features for solely the 10 bp regions flanking this feature.
205 $ bin/flankBed -i a.bed -b 10 -g genomes/human.hg18.genome
206 chr1 90 100
207 chr1 200 210
208
209 In contrast, slopBed would return:
210 bin/slopBed -i a.bed -b 10 -g genomes/human.hg18.genome
211 chr1 90 210
212
213 FlankBed has all of the same features as slopBed.
214
215
216 New Features
217 ============
218 1. Added new "-scores" feature to mergeBed. This allows one to take the sum, min, max,
219 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.
220 2. mergeBed now tolerates multiple features in a merged block to have the same feature name.
221 3. Thanks to Erik Garrison's "fastahack" library, fastaFromBed now reports its output in the order of the input file.
222 4. Added a "-n" option to bed12ToBed6, which forces the score field to be the 1-based block number from the original BED12 feature. This is useful for tracking exon numbers, for example.
223 5. Thanks to Can Alkan, added a new "-mc" option to maskFastaFromBed that allows one to define a custom mask character, such as "X" (-n X).
224
225
226 Bug Fixes
227 =========
228 1. Thanks to Davide Cittaro, intersectBed and windowBed now properly capture unmapped BAM alignments when using the "-v" option.
229 2. ClosestBed now properly handles cases where b.end == a.start
230 3. Thanks to John Marshall, the default constructors are much safer and less buggy.
231 4. Fixed bug in shuffleBed that complained about a lack of -incl and -excl.
232 5. Fixed bug in shuffleBed for features that would go beyond the end of a chromosome.
233 6. Tweaked bedToIgv to make it more Windows friendly.
234
235
236
237 Version 2.11.2 (January-31-2010)
238 Fixed a coordinate reporting bug in coverageBed.
239 Added "max distance (-d)" argument back to the new implementation of mergeBed.
240
241
242
243 Version 2.11.0 (January-21-2010)
244
245 Enhancements:
246 =============
247 1. Support for zero length features (i.e., start = end)
248 - For example, this allows overlaps to be detected with insertions in the reference genome, as reported by dbSNP.
249 2. Both 8 and 9 column GFF files are now supported.
250 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.
251 4. Two improvements to shuffleBed:
252 3a. A -f (overlapFraction) parameter that defines the maximum overlap that a randomized feature can have with an -excl feature.
253 That is, if a chosen locus has more than -f overlap with an -excl feature, a new locus is sought.
254 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
255 that a randomized feature does not go beyond the end of a chromosome.
256 5. bamToBed can now optionally report the CIGAR string as an additional field.
257 6. pairToPair can now report the entire paired feature from the B file when overlaps are found.
258 7. complementBed now reports all chromosomes, not just those with features in the BED file.
259 8. Improved randomization seeding in shuffleBed. This prevents identical output for runs of shuffleBed that
260 occur in the same second (often the case).
261
262
263 Bug Fixes:
264 ==========
265 1. Fixed the "BamAlignmentSupportData is private" compilation issue.
266 2. Fixed a bug in windowBed that caused positions to run off the end of a chromosome.
267
268
269 Major Changes:
270 ==============
271 1. The groupBy command is now part of the filo package (https://github.com/arq5x/filo) and will no longer be distributed with BEDTools.
272
273
274
275 Version 2.10.0 (September-21-2010)
276 ==New tools==
277 1. annotateBed. Annotates one BED/VCF/GFF file with the coverage and number of overlaps observed
278 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.
279 $ annotateBed -i variants.bed -files genes.bed conserv.bed known_var.bed
280
281 This tool was suggested by Can Alkan and was motivated by the example source code that he kindly provided.
282
283 ==New features==
284 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.
285 2. Support for writing uncompressed bam with the -ubam option.
286 3. Shorthand arguments for groupBy (-g eq. -grp, -c eq. -opCols, -o eq. -opCols).
287 4. In addition, all BEDTools that require only one main input file (the -i file) will assume that input is
288 coming from standard input if the -i parameter is ignored. For example, the following are equivalent:
289 $ cat snps.bed | sortBed –i stdin
290 $ cat snps.bed | sortBed
291
292 As are these:
293 $ cat data.txt | groupBy -i stdin -g 1,2,3 -c 5 -o mean
294 $ cat data.txt | groupBy -g 1,2,3 -c 5 -o mean
295
296 ==Bug fixes==
297 1. Increased the precision of the output from groupBy.
298
299
300
301 Version 2.9.0 (August-16-2010)
302 ==New tools==
303 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.
304
305 ==New features==
306 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.
307 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).
308
309
310 ==Bug Fixes==
311 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.
312 2. Fixed minor reporting annoyances in closestBed. Thanks to Erik Arner.
313 3. Fixed typo/bug in genomeCoverageBed that reported negative coverage owing to numeric overflow. Thanks to Alexander Dobin for the detailed bug report.
314 4. Fixed other minor parsing and reporting bugs/annoyances.
315
316
317
318
319 Version 2.8.3 (July-25-2010)
320 1. Fixed bug that caused some GFF files to be misinterpreted as VCF. This prevented the detection of overlaps.
321 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".
322 3. Updated the BamTools API.
323
324
325 Version 2.8.2 (July-18-2010)
326 1. Fixed a bug in bedFile.h preventing GFF strands from being read properly.
327 2. Fixed a bug in intersectBed that occasionally caused spurious overlaps between BAM alignments and BED features.
328 3. Fixed bug in intersectBed causing -r to not report the same result when files are swapped.
329 4. Added checks to groupBy to prevent the selection of improper opCols and groups.
330 5. Fixed various compilation issues, esp. for groupBy, bedToBam, and bedToIgv.
331 6. Updated the usage statements to reflect bed/gff/vcf support.
332 7. Added new fileType functions for auto-detecting gzipped or regular files. Thanks to Assaf Gordon.
333
334
335 Version 2.8.1 (July-05-2010)
336 1. Added bedToIgv.
337
338
339 Version 2.8.0 (July-04-2010)
340
341 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.
342
343 2. Added native support for the 1000 Genome Variant Calling Format (VCF) version 4.0.
344
345 3. New bed12ToBed6 tool. This tool will convert each block of a BED12 feature into discrete BED6 features.
346
347 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 functionality in groupBy was motivated by helpful discussions with Erik Arner at Riken.
348
349 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.
350
351 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.
352
353 7. Fixed a careless bug in slopBed also found by Erik Arner (Riken) that caused an infinite loop when the "-excl" option was used.
354
355 8. Reduced memory consumption by ca. 15% and run time by ca. 10% for most tools.
356
357 9. Several code-cleanliness updates such as templated functions and common tyedefs.
358
359 10. Tweaked the genome binning approach such that 16kb bins are the most granular.
360
361
362 Version 2.7.1 (May-06-2010)
363 Fixed a typo that caused some compilers to fail on closestBed.
364
365 Version 2.7.0 (May-05-2010)
366
367 General:
368 1. "Gzipped" BED and GFF files are now supported as input by all BEDTools. Such files must end in ".gz".
369 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.
370 3. bamToBed requires the BAM file to be sorted/grouped by read id when creating BEDPE output. This allows the alignments end coordinate for each end of the pair to be properly computed based on its CIGAR string. The same requirement applies to pairToBed.
371 4. Updated manual.
372 5. Many silent modifications to the code that improve clarity and sanity-checking and facilitate future additions/modifications.
373
374
375 New Tools:
376 1. bedToBam. This utility will convert BED files to BAM format. Both "blocked" (aka BED12) and "unblocked" (e.g. BED6) formats are acceptable. This allows one to, for example, compress large BED files such as dbSNP into BAM format for efficient visualization.
377
378
379 Changes to existing tools:
380 intersectBed
381 1. Added -wao option to report 0 overlap for features in A that do not intersect any features in B. This is an extension of the -wo option.
382
383 bamToBed
384 1. Requires that BAM input be sorted/grouped by read name.
385
386 pairToBed
387 1. Requires that BAM input be sorted/grouped by read name.
388 2. Allows use of minimum mapping quality or total edit distance for score field.
389
390 windowBed
391 1. Now supports BAM input.
392
393 genomeCoverageBed
394 1. -bga option. Thanks to Gordon Assaf for the suggestion.
395 2. Eliminated potential seg fault.
396
397 Acknowledgements:
398 1. Gordon Assaf: for suggesting the -bga option in genomeCoverageBed and for testing the new bedToBam utility.
399 2. Ivan Gregoretti: for helping to expedite the inclusion of gzip support.
400 3. Can Alkan: for suggesting the addition of the -wao option to intersectBed.
401 4. James Ward: for pointing out that bedToBam did not need to create "dummy" seq and qual entries.
402
403
404
405 Version 2.6.1 (Mar-29-2010)
406 1. Fixed a careless command line parsing bug in coverageBed.
407
408
409 Version 2.6.0 (Mar-23-2010)
410 ***Specific improvements / additions to tools***
411 1. intersectBed
412 * Added an option (-wo) that reports the number of overlapping bases for each intersection b/w A and B files.
413 -- Not sure why this wasn't added sooner; it's obvious.
414
415 2. coverageBed
416 * native BAM support
417 * can now report a histogram (-hist) of coverage for each feature in B. Useful for exome sequencing projects, for example.
418 -- thanks for the excellent suggestion from Jose Bras
419 * faster
420
421 3. genomeCoverageBed
422 * native BAM support
423 * can now report coverage in BEDGRAPH format (-bg)
424 -- thanks for the code and great suggestion from Gordon Assaf, CSHL.
425
426 4. bamToBed
427 * support for "blocked" BED (aka BED12) format. This facilitates the creation of BED entries for "split" alignments (e.g. RNAseq or SV)
428 -- thanks to Ann Loraine, UNCC for test data to support this addition.
429
430 5. fastaFromBed
431 * 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.
432 -- thanks to Thomas Doktor, U. of Southern Denmark for the code and suggestion.
433
434 6. ***NEW*** overlap
435 * newly added tool for computing the overlap/distance between features on the same line.
436 -- For example:
437 $ cat test.out
438 chr1 10 20 A chr1 15 25 B
439 chr1 10 20 C chr1 25 35 D
440
441 $ cat test.out | overlaps -i stdin -cols 2,3,6,7
442 chr1 10 20 A chr1 15 25 B 5
443 chr1 10 20 C chr1 25 35 D -5
444
445 ***Bug fixes***
446 1. Fixed a bug in pairToBed when comparing paired-end BAM alignments to BED annotations and using the "notboth" option.
447 2. Fixed an idiotic bug in intersectBed that occasionally caused segfaults when blank lines existed in BED files.
448 3. Fixed a minor bug in mergeBed when using the -nms option.
449
450 ***General changes***
451 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.
452 2. Cleaned up some of the code and made the API a bit more streamlined. Will facilitate future tool development, etc.
453
454
455 Version 2.5.4 (Mar-3-2010)
456 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!
457
458
459 Version 2.5.3 (Feb-19-2010)
460 1. Fixed bug to "re-allow" track and "browser" lines.
461 2. Fixed bug in reporting BEDPE overlaps.
462 3. Fixed bug when using type "notboth" with BAM files in pairToBed.
463 4. When comparing BAM files to BED/GFF annotations with intersectBed or pairToBed, the __aligned__ sequence is used, rather than the __original__ sequence.
464 5. Greatly increased the speed of pairToBed when using BAM alignments.
465 6. Fixed a bug in bamToBed when reporting edit distance from certain aligners.
466
467
468 Version 2.5.2 (Feb-2-2010)
469 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.
470 2. Added an error message to mergeBed preventing one from using "-n" and "-nms" together.
471 3. Fixed a bug in pairToBed that caused neither -type "notispan" nor "notospan" to behave as described.
472
473
474 Version 2.5.1 (Jan-28-2010)
475 1. Fixed a bug in the new GFF/BED determinator that caused a segfault when start = 0.
476
477
478 Version 2.5.0 (Jan-27-2010)
479 1. Added support for custom BED fields after the 6th column.
480 2. Fixed a command line parsing bug in pairToBed.
481 3. Improved sanity checking.
482
483
484 Version 2.4.2 (Jan-23-2010)
485 1. Fixed a minor bug in mergeBed when -nms and -s were used together.
486 2. Improved the command line parsing to prevent the occasional segfault.
487
488
489 Version 2.4.1 (Jan-12-2010)
490 1. Updated BamTools libraries to remove some compilation issues on some systems/compilers.
491
492
493 Version 2.4.0 (Jan-11-2010)
494 1. Added BAM support to intersectBed and pairToBed
495 2. New bamToBed feature.
496 3. Added support for GFF features
497 4. Added support for "blocked" BED format (BED12)
498 6. Wrote complete manual and included it in distribution.
499 7. Fixed several minor bugs.
500 8. Cleaned up code and improved documentation.
501
502
503 Version 2.3.3 (12/17/2009)
504 Rewrote complementBed to use a slower but much simpler approach. This resolves several bugs with the previous logic.
505
506
507 Version 2.3.2 (11/25/2009)
508 Fixed a bug in subtractBed that prevent a file from subtracting itself when the following is used:
509 $ subtractBed -a test.bed -b test.bed
510
511
512 Version 2.3.1 (11/19/2009)
513 Fixed a typo in closestBed that caused all nearby features to be returned instead of just the closest one.
514
515
516 Version 2.3.0 (11/18/2009)
517 1. Added four new tools:
518 - shuffleBed. Randomly permutes the locations of a BED file among a genome. Useful for testing for significant overlap enrichments.
519 - slopBed. Adds a requested number of base pairs to each end of a BED feature. Constrained by the size of each chromosome.
520 - maskFastaFromBed. Masks a FASTA file based on BED coordinates. Useful making custom genome files from targeted capture experiment, etc.
521 - pairToPair. Returns overlaps between two paired-end BED files. This is great for finding structural variants that are private or shared among samples.
522
523 2. Increased the speed of intersectBed by nearly 50%.
524 3. Improved corrected some of the help messages.
525 4. Improved sanity checking for BED entries.
526
527
528 Version 2.2.4 (10/27/2009)
529 1. Updated the mergeBed documentation to describe the -names option which allows one to report the names of the
530 features that were merged (separated by semicolons).
531
532
533 Version 2.2.3 (10/23/2009)
534 1. Changed windowBed to optionally define "left" and "right" windows based on strand. For example by default, -l 100 and -r 500 will
535 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).
536
537 However if one chooses the -sw option (windows bases on strandedness), the behavior changes. Assume the above example except that a feature in A
538 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).
539
540 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.
541
542 ***NOTE: This replaces the previous -s option and may affect existing pipelines***.
543
544
545 Version 2.2.2 (10/20/2009)
546 1. Improved the speed of genomeCoverageBed by roughly 100 fold. The memory usage is now less than 2.0 Gb.
547
548
549 Version 2.2.1
550 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.
551 Many thanks to folks in the Hannon lab at CSHL for pointing this out.
552
553
554 Version 2.2.0
555 === Notable changes in this release ===
556 1. coverageBed will optionally only count features in BED file A (e.g. sequencing reads) that overlap with
557 the intervals/windows in BED file B on the same strand. This has been requested several times recently
558 and facilitates CHiP-Seq and RNA-Seq experiments.
559
560 2. intersectBed can now require a minimum __reciprocal__ overlap between intervals in BED A and BED B. For example,
561 previously, if one used -f 0.90, it required that a feature in B overlap 90% of the feature in A for the "hit"
562 to be reported. If one adds the -r (reciprocal) option, the hit must also cover 90% of the feature in B. This helps
563 to exclude overlaps between say small features in A and large features in B:
564
565 A ==========
566 B **********************************************************
567
568 -f 0.50 (Reported), whereas -f 0.50 -r (Not reported)
569
570 3. The score field has been changed to be a string. While this deviates from the UCSC definition, it allows one to track
571 much more meaningful information about a feature/interval. For example, score could now be:
572
573 7.31E-05 (a p-value)
574 0.334577 (mean enrichment)
575 2:2.2:40:2 (several values encoded in a string)
576
577 4. closestBed now, by default, reports __all__ intervals in B that overlap equally with an interval in A. Previously, it
578 merely reported the first such feature that appeared in B. Here's a cartoon explaining the difference.
579
580 **Prior behavior**
581
582 A ==============
583 B.1 ++++++++++++++
584 B.2 ++++++++++++++
585 B.3 +++++++++
586
587 -----------------------------------------
588 Result = B.1 ++++++++++++++
589
590
591 **Current behavior**
592
593 A ==============
594 B.1 ++++++++++++++
595 B.2 ++++++++++++++
596 B.3 +++++++++
597
598 -----------------------------------------
599 Result = B.1 ++++++++++++++
600 B.2 ++++++++++++++
601
602 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.
603
604 5. Several other minor changes to the algorithms have been made to increase speed a bit.
605
606
607 VERSION 2.1.2
608 1. Fixed yet another bug in the parsing of "track" or "browser" lines. Sigh...
609 2. Change the "score" column (i.e. column 5) to b stored as a string. While this deviates
610 from the UCSC convention, it allows significantly more information to be packed into the column.
611
612
613 VERSION 2.1.1
614 1. Added limits.h to bedFile.h to fix compilation issues on some systems.
615 2. Fixed bug in testing for "track" or "browser" lines.
616
617
618 VERSION 2.1.0
619 1. Fixed a bug in peIntersectBed that prevented -a from being correctly handled when passed via stdin.
620 2. Added new functionality to coverageBed that calculates the density of coverage.
621 3. Fixed bug in geneomCoverageBed.
622
623
624 VERSION 2.0.1
625 1. Added the ability to retain UCSC browser track/browser headers in BED files.
626
627
628 VERSION 2.0
629 1. Sped up the file parsing. ~10-20% increase in speed.
630 2. Created reportBed() as a common method in the bedFile class. Cleans up the code quite nicely.
631 3. Added the ability to compare BED files accounting for strandedness.
632 4. Paired-end intersect.
633 5. Fixed bug that prevented overlaps from being reported when the overlap fraction requested is 1.0
634
635
636
637 VERSION 1.2, 04/27/2009. (1eb06115bdf3c49e75793f764a70c3501bb53f33)
638 1. Added subtractBed.
639 A. Fixed bug that prevented "split" overlaps from being reported.
640 B. Prevented A from being reported if >=1 feature in B completely spans it.
641 2. Added linksBed.
642 3. Added the ability to define separate windows for upstream and downstream to windowBed.
643
644
645 VERSION 1.1, 04/23/2009. (b74eb1afddca9b70bfa90ba763d4f2981a56f432)
646 Initial release.