From 5d29b3c08264ff3f81eb06054b18ea9939b2f51f Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 4 Jan 2010 14:06:12 -0500
Subject: [PATCH] Command line option formatting standardized.

---
 bin/coverageBed                               | Bin 89904 -> 89904 bytes
 bin/fastaFromBed                              | Bin 90760 -> 90760 bytes
 bin/genomeCoverageBed                         | Bin 112440 -> 112440 bytes
 bin/linksBed                                  | Bin 95360 -> 95360 bytes
 bin/maskFastaFromBed                          | Bin 95264 -> 95264 bytes
 bin/pairToBed                                 | Bin 176872 -> 176872 bytes
 bin/pairToPair                                | Bin 113728 -> 113728 bytes
 bin/shuffleBed                                | Bin 104168 -> 104168 bytes
 bin/slopBed                                   | Bin 95368 -> 95368 bytes
 genomes/mouse.mm8.genome                      |  35 ++
 genomes/mouse.mm9.genome                      |  36 ++
 log                                           | 437 ++++++++++++++++++
 obj/coverageMain.o                            | Bin 7356 -> 7356 bytes
 obj/fastaFromBedMain.o                        | Bin 6552 -> 6552 bytes
 obj/genomeCoverageMain.o                      | Bin 8660 -> 8652 bytes
 obj/linksMain.o                               | Bin 8884 -> 8860 bytes
 obj/maskFastaFromBedMain.o                    | Bin 6664 -> 6656 bytes
 obj/pairToBedMain.o                           | Bin 12496 -> 12552 bytes
 obj/pairToPairMain.o                          | Bin 8868 -> 8884 bytes
 obj/shuffleBedMain.o                          | Bin 9164 -> 9156 bytes
 obj/slopBedMain.o                             | Bin 10440 -> 10408 bytes
 src/coverageBed/coverageMain.cpp              |   2 +-
 src/fastaFromBed/fastaFromBedMain.cpp         |   4 +-
 src/genomeCoverageBed/genomeCoverageMain.cpp  |   8 +-
 src/intersectBed/a.bed                        |   1 +
 src/intersectBed/b.bed                        |   2 +-
 src/linksBed/linksMain.cpp                    |   6 +-
 src/maskFastaFromBed/maskFastaFromBedMain.cpp |   6 +-
 src/pairToBed/pairToBedMain.cpp               |   6 +-
 src/pairToPair/pairToPairMain.cpp             |   8 +-
 src/shuffleBed/shuffleBedMain.cpp             |   8 +-
 src/slopBed/slopBedMain.cpp                   |  10 +-
 32 files changed, 539 insertions(+), 30 deletions(-)
 create mode 100644 genomes/mouse.mm8.genome
 create mode 100644 genomes/mouse.mm9.genome
 create mode 100644 log

diff --git a/bin/coverageBed b/bin/coverageBed
index eee6e34538a4a9bf4697f901c0cc8b386749b7b9..0b0692ca1097bdf6f07e74841ef53dbb8ea46f21 100755
GIT binary patch
delta 53
zcmdn6k97kOC9nxhVbA?}rRa5M=!tb!shdx(+FZa^C&(x<`MtOn<D<<|5@)whesNx7
JGyes}egLEc80-K5

delta 53
zcmdn6k97kOC9nxxn6@r!?t5E{i+;0}vmVc$vblh*PLNS@@_TVD#>bnbB+hQ1{Or8u
JW`PR|{Q#L~7<vEz

diff --git a/bin/fastaFromBed b/bin/fastaFromBed
index 7063e23e96e2e06d91285bf59b473cac583c2ace..be388680a3e541caa9ffb03ff17fd4db3c7cff7f 100755
GIT binary patch
delta 90
zcmeA;%Gz<1bwdK1fZkl~mIu~z1roQvjWqdiqI+`zTOBK-=;Zg@=8R&S)p_I&3wq`i
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delta 90
zcmeA;%Gz<1bwdK1Kzp%(q=HHK<Q;sS3Y!-B9oSsJR>#UHHu*ibIivVybso9Hf}Eat
j1*IhlZjQkrjtXg+IjNJw&YK8v`j?iV3U8is{>>x+jRzoK

diff --git a/bin/genomeCoverageBed b/bin/genomeCoverageBed
index d597ce6e93355c1a5f8eb2ca51c7b4d55af0f5dc..cc39fb5ceb10d1772e10fa76cc5e3192ecd9acc6 100755
GIT binary patch
delta 8165
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diff --git a/bin/linksBed b/bin/linksBed
index 3430a144ad06c4cd6be62be00f51b3c7b62a63de..d8964988051cdc4fe281417da3e7ec93f59690d0 100755
GIT binary patch
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delta 7645
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fu9^!i<{3!s%wLMUnhjleun@Pp?tA$e=oI~bP`g@N

diff --git a/bin/maskFastaFromBed b/bin/maskFastaFromBed
index 90cb6dbed12aef22eddbe8fe67f7f3d999e1806a..83b1d0e4249e288c250108a4a8f14220648de49e 100755
GIT binary patch
delta 817
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ztf-Y|U(T*w{h&r8^Y<K9sm7zZ>2<Oht4|_2lK(Nc{E8M0-Bjy&(c%9XuHXj#t;f*2
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DR^T&@

delta 822
zcmZ9KZA^_}7{{Og<J26gp$><(o~KiZIw$h7MqX!~p7UZyClpg_(Hl-e5wb9r!xFAl
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diff --git a/bin/pairToBed b/bin/pairToBed
index c5a4f41d66812e3aa97ebd6d203f9169336a464c..bd19f8e101c232886d7a99e4388c700748516384 100755
GIT binary patch
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diff --git a/bin/pairToPair b/bin/pairToPair
index c50b5e5122e7e52b11e2476cb160654a2ae3b4ed..3a2ede01fae21d0f18f07aadb92f5de4467dcd30 100755
GIT binary patch
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diff --git a/bin/shuffleBed b/bin/shuffleBed
index 759bf6205863981d56b0e9820d4a0912e786a8dd..d990a9e0f33bf81f771f3c6aeafde765344f26c6 100755
GIT binary patch
delta 7909
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diff --git a/bin/slopBed b/bin/slopBed
index 69ad500cd13b64b64b4500c4630afae8ee1e4a0c..4ab09549b1320598f56f7f089ecb61cddf9c6cbc 100755
GIT binary patch
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diff --git a/genomes/mouse.mm8.genome b/genomes/mouse.mm8.genome
new file mode 100644
index 00000000..904ce1eb
--- /dev/null
+++ b/genomes/mouse.mm8.genome
@@ -0,0 +1,35 @@
+chr1	197069962
+chr2	181976762
+chr3	159872112
+chr4	155029701
+chr5	152003063
+chr6	149525685
+chr7	145134094
+chr8	132085098
+chr9	124000669
+chrM	16299
+chrX	165556469
+chrY	16029404
+chr10	129959148
+chr11	121798632
+chr12	120463159
+chr13	120614378
+chr14	123978870
+chr15	103492577
+chr16	98252459
+chr17	95177420
+chr18	90736837
+chr19	61321190
+chr1_random	172274
+chr5_random	2921247
+chr7_random	243910
+chr8_random	206961
+chr9_random	17232
+chrX_random	39696
+chrY_random	14577732
+chr10_random	10781
+chr13_random	436191
+chr15_random	105932
+chr17_random	89091
+chrUn_random	1540053
+
diff --git a/genomes/mouse.mm9.genome b/genomes/mouse.mm9.genome
new file mode 100644
index 00000000..84c1e724
--- /dev/null
+++ b/genomes/mouse.mm9.genome
@@ -0,0 +1,36 @@
+chr1	197195432
+chr2	181748087
+chr3	159599783
+chr4	155630120
+chr5	152537259
+chr6	149517037
+chr7	152524553
+chr8	131738871
+chr9	124076172
+chr10	129993255
+chr11	121843856
+chr12	121257530
+chr13	120284312
+chr14	125194864
+chr15	103494974
+chr16	98319150
+chr17	95272651
+chr18	90772031
+chr19	61342430
+chrX	166650296
+chrY	15902555
+chrM	16299
+chr13_random	400311
+chr16_random	3994
+chr17_random	628739
+chr1_random	1231697
+chr3_random	41899
+chr4_random	160594
+chr5_random	357350
+chr7_random	362490
+chr8_random	849593
+chr9_random	449403
+chrUn_random	5900358
+chrX_random	1785075
+chrY_random	58682461
+
diff --git a/log b/log
new file mode 100644
index 00000000..86977814
--- /dev/null
+++ b/log
@@ -0,0 +1,437 @@
+
+Program: bamToBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Converts BAM alignments to BED6 or BEDPE format.
+
+Usage:   bamToBed [OPTIONS] -i <bam> 
+
+Options: 
+	-bedpe	Write BEDPE format.
+
+	-ed	Use BAM edit distance (NM tag) for score.
+		Default is to use mapping quality.
+		Not available for BEDPE format.
+
+
+Program: closestBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: For each feature in BED A, finds the closest 
+		 feature (upstream or downstream) in BED B.
+
+Usage:   closestBed [OPTIONS] -a <a.bed> -b <b.bed>
+
+Options: 
+	-s	Force strandedness.  That is, find the closest feature in B
+		that overlaps A on the same strand.
+		- By default, overlaps are reported without respect to strand.
+
+	-t	How ties for closest feature are handled.  This occurs when two
+		features in B have exactly the same overlap with A.
+		By default, all such features in B are reported.
+		Here are all the options:
+		- "all"  Report all ties (default).
+		- "first"  Report the first tie that occurred in the B file.
+		- "last"  Report the last tie that occurred in the B file.
+
+Notes: 
+	Reports "none" for chrom and "-1" for all other fields when a feature
+	is not found in B on the same chromosome as the feature in A.
+	E.g. none	-1	-1
+
+
+Program: complementBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Returns the base pair complement of a BED file.
+
+Usage:   complementBed [OPTIONS] -i <bed> -g <genome>
+
+Notes: 
+	(1)  The genome file should tab delimited and structured as follows:
+	     <chromName><TAB><chromSize>
+
+	For example, Human (hg19):
+	chr1	249250621
+	chr2	243199373
+	...
+	chr18_gl000207_random	4262
+
+Tips: 
+	One can use the UCSC Genome Browser's MySQL database to extract
+	chromosome sizes. For example, H. sapiens:
+
+	mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e /
+	"select chrom, size from hg19.chromInfo"  > hg19.genome
+
+
+Program: coverageBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Returns the depth and breadth of coverage of features from A
+		 on the intervals in B.
+
+Usage:   coverageBed [OPTIONS] -a <a.bed> -b <b.bed>
+
+Options: 
+	-s	Force strandedness.  That is, only include hits in A that
+		overlap B on the same strand.
+		- By default, hits are included without respect to strand.
+
+Output:  
+	 After each entry in B, reports: 
+	  1) The number of features in A that overlapped the B interval.
+	  2) The number of bases in B that had non-zero coverage.
+	  3) The length of the entry in B.
+	  4) The fraction of bases in B that had non-zero coverage.
+
+Program: fastaFromBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Extract DNA sequences into a fasta file based on BED coordinates.
+
+Usage:   fastaFromBed [OPTIONS] -fi -bed -fo 
+
+Options: 
+	-fi		Input FASTA file
+	-bed	BED file of ranges to extract from -fi
+	-fo		Output FASTA file
+	-name	Use the BED name field (#4) for the FASTA header
+
+Program: genomeCoverageBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Compute the coverage of a BED file among a genome.
+
+Usage:   genomeCoverageBed [OPTIONS] -i <bed> -g <genome>
+
+Options: 
+	-d		Report the depth at each genome position.
+			Default behavior is to report a histogram.
+
+	-max	Combine all positions with a depth >= max into
+			a single bin in the histogram.
+			- (INTEGER)
+
+Notes: 
+	(1)  The genome file should tab delimited and structured as follows:
+	     <chromName><TAB><chromSize>
+
+	For example, Human (hg19):
+	chr1	249250621
+	chr2	243199373
+	...
+	chr18_gl000207_random	4262
+
+	(2)  NOTE: The input BED file must be grouped by chromosome.
+	     A simple "sort -k 1,1 <BED> > <BED>.sorted" will suffice.
+
+Tips: 
+	One can use the UCSC Genome Browser's MySQL database to extract
+	chromosome sizes. For example, H. sapiens:
+
+	mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e /
+	"select chrom, size from hg19.chromInfo"  > hg19.genome
+
+
+Program: intersectBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Report overlaps between a.bed and b.bed.
+
+Usage:   intersectBed [OPTIONS] -a <a.bed> -b <b.bed>
+
+Options: 
+	-abam	The A input file is in BAM format.  Output will be BAM as well.
+
+	-outbam	Write output as BAM. This will report those BAM alignments.
+		that meet the intersect criteria.  BAM entry is written once.
+
+	-wa	Write the original entry in A for each overlap.
+
+	-wb	Write the original entry in B for each overlap.
+		- Useful for knowing _what_ A overlaps. Restricted by -f.
+
+	-u	Write the original A entry _once_ if _any_ overlaps found in B.
+		- In other words, just report the fact >=1 hit was found.
+
+	-c	For each entry in A, report the number of overlaps with B.
+		- Reports 0 for A entries that have no overlap with B.
+		- Overlaps restricted by -f.
+
+	-v	Only report those entries in A that have _no overlaps_ with B.
+		- Similar to "grep -v."
+
+	-f	Minimum overlap required as a fraction of A.
+		- Default is 1E-9 (i.e., 1bp).
+		- FLOAT (e.g. 0.50)
+
+	-r	Require that the fraction overlap be reciprocal for A and B.
+		- In other words, if -f is 0.90 and -r is used, this requires
+		  that B overlap 90% of A and A _also_ overlaps 90% of B.
+
+	-s	Force strandedness.  That is, only report hits in B that
+		overlap A on the same strand.
+		- By default, overlaps are reported without respect to strand.
+
+
+Program: linksBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Creates HTML links to an UCSC Genome Browser from a BED file.
+
+Usage:   linksBed [OPTIONS] -i <input.bed> > out.html
+
+Options: 
+	-base	The browser basename.  Default: http://genome.ucsc.edu 
+	-org	The organism. Default: human
+	-db		The build.  Default: hg18
+
+Example: 
+	By default, the links created will point to the human (hg18) UCSC browser.
+	If you have a local mirror, you can override this behavior by supplying
+	the -base, -org, and -db options.
+
+	For example, if the main URL of your local mirror for mouse MM9 is called: 
+	http://mymirror.myuniversity.edu, then you would use the following:
+	-base http://mymirror.myuniversity.edu
+	-org mouse
+	-db mm9
+
+Program: maskFastaFromBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Mask a fasta file based on BED coordinates.
+
+Usage:   maskFastaFromBed [OPTIONS] -fi -out -bed
+
+Options:
+	-fi		Input FASTA file
+	-bed	BED file of ranges to mask in -fi
+	-fo		Output FASTA file
+	-soft	Enforce "soft" masking.  That is, instead of masking with Ns,
+			mask with lower-case bases.
+
+Program: mergeBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Merges overlapping BED entries into a single interval.
+
+Usage:   mergeBed [OPTIONS] -i <input.bed>
+
+Options: 
+	-s	Force strandedness.  That is, only merge features
+		that are the same strand.
+		- By default, merging is done without respect to strand.
+
+	-n	Report the number of BED entries that were merged.
+		- Note: "1" is reported if no merging occurred.
+
+	-d	Maximum distance between features allowed for features
+		to be merged.
+		- Def. 0. That is, overlapping & book-ended features are merged.
+		- (INTEGER)
+
+	-nms	Report the names of the merged features separated by semicolons.
+
+
+Program: pairToBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Report overlaps between a BEDPE file and a BED file.
+
+Usage:   pairToBed [OPTIONS] -a <BEDPE> -b <BED>
+
+Options: 
+	-abam	The A input file is in BAM format.  Output will be BAM as well.
+
+	-outbam	Write output as BAM. This will report those BAM alignments.
+		that meet the intersect criteria.  BAM entry is written once.
+
+	-f	Minimum overlap required as fraction of A (e.g. 0.05).
+		Default is 1E-9 (effectively 1bp).
+
+	-s	Enforce strandedness when finding overlaps.
+		Default is to ignore stand.
+		Not applicable with -type inspan or -type outspan.
+
+	-type 	Approach to reporting overlaps between BEDPE and BED.
+
+		either	Report overlaps if either end of A overlaps B.
+			- Default.
+		neither	Report A if neither end of A overlaps B.
+		both	Report overlaps if both ends of A overlap  B.
+		xor	Report overlaps if one and only one end of A overlaps B.
+		ispan	Report overlaps between [end1, start2] of A and B.
+			- Note: If chrom1 <> chrom2, entry is ignored.
+		ospan	Report overlaps between [start1, end2] of A and B.
+			- Note: If chrom1 <> chrom2, entry is ignored.
+
+		notispan	Report A if ispan of A doesn't overlap B.
+			- Note: If chrom1 <> chrom2, entry is ignored.
+		notospan	Report A if ospan of A doesn't overlap B.
+			- Note: If chrom1 <> chrom2, entry is ignored.
+
+Refer to the BEDTools manual for BEDPE format.
+
+
+Program: pairToPair (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Report overlaps between two paired-end BED files (BEDPE).
+
+Usage:   pairToPair [OPTIONS] -a <BEDPE> -b <BEDPE>
+
+Options: 
+	-f	Minimum overlap required as fraction of A (e.g. 0.05).
+		Default is 1E-9 (effectively 1bp).
+
+	-type 	Approach to reporting overlaps between A and B.
+		neither		Report overlaps if neither end of A overlaps B.
+
+		both		Report overlaps if both ends of A overlap B.
+				- Default.
+	-is	Ignore strands when searching for overlaps.
+		- By default, strands are enforced.
+
+Refer to the BEDTools manual for BEDPE format.
+
+
+Program: shuffleBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Randomly permute the locations of a BED file among a genome.
+
+Usage:   shuffleBed [OPTIONS] -g <genome> -i <bed>
+
+Options: 
+	-excl	A BED file of coordinates in which features in -i
+			should not be placed (e.g. gaps.bed).
+
+	-chrom	Keep features in -i on the same chromosome.
+			- By default, the chrom and position are randomly chosen.
+
+	-seed	Supply an integer seed for the shuffling.
+			- By default, the seed is chosen automatically.
+			- (INTEGER)
+
+Notes: 
+	(1)  The genome file should tab delimited and structured as follows:
+	     <chromName><TAB><chromSize>
+
+	For example, Human (hg19):
+	chr1	249250621
+	chr2	243199373
+	...
+	chr18_gl000207_random	4262
+
+Tips: 
+	One can use the UCSC Genome Browser's MySQL database to extract
+	chromosome sizes. For example, H. sapiens:
+
+	mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e /
+	"select chrom, size from hg19.chromInfo"  > hg19.genome
+
+
+Program: slopBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Add requested base pairs of "slop" to each BED entry.
+
+Usage:   slopBed [OPTIONS] -i <bed> -g <genome> [-b <int> or (-l and -r)]
+
+Options: 
+	-b	Increase the BED entry by the same number base pairs in each direction.
+		- (Integer)
+	-l	The number of base pairs to subtract from the start coordinate.
+		- (Integer)
+	-r	The number of base pairs to add to the end coordinate.
+		- (Integer)
+	-s	Define -l and -r based on strand.
+		E.g. if used, -l 500 for a negative-stranded feature, 
+		it will add 500 bp downstream.  Default = false.
+
+Notes: 
+	(1)  Starts will be set to 0 if the requested slop would force it below 0.
+	(2)  Ends will be set to the chromosome length if the requested slop would
+		 force it above the max chrom length.
+	(3)  The genome file should tab delimited and structured as follows:
+	     <chromName><TAB><chromSize>
+
+	For example, Human (hg19):
+	chr1	249250621
+	chr2	243199373
+	...
+	chr18_gl000207_random	4262
+
+Tips: 
+	One can use the UCSC Genome Browser's MySQL database to extract
+	chromosome sizes. For example, H. sapiens:
+
+	mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e /
+	"select chrom, size from hg19.chromInfo"  > hg19.genome
+
+
+Program: sortBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Sorts a BED file in various and useful ways.
+
+Usage:   sortBed [OPTIONS] -i <input.bed>
+
+Options: 
+	-sizeA		Sort by feature size in ascending order.
+	-sizeD		Sort by feature size in descending order.
+	-chrThenSizeA	Sort by chrom (asc), then feature size (asc).
+	-chrThenSizeD	Sort by chrom (asc), then feature size (desc).
+	-chrThenScoreA	Sort by chrom (asc), then score (asc).
+	-chrThenScoreD	Sort by chrom (asc), then score (desc).
+
+
+Program: subtractBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Removes the portion(s) of an interval that is overlapped
+		 by another feature(s).
+
+Usage:   subtractBed [OPTIONS] -a <a.bed> -b <b.bed>
+
+Options: 
+	-f	Minimum overlap required as a fraction of A.
+		- Default is 1E-9 (i.e., 1bp).
+		- (FLOAT) (e.g. 0.50)
+
+	-s	Force strandedness.  That is, only report hits in B that
+		overlap A on the same strand.
+		- By default, overlaps are reported without respect to strand.
+
+
+Program: windowBed (v2.3.3)
+Author:  Aaron Quinlan (aaronquinlan@gmail.com)
+Summary: Examines a "window" around each feature in A and
+		 reports all features in B that overlap the window. For each
+		 overlap the entire entry in A and B are reported.
+
+Usage:   windowBed [OPTIONS] -a <a.bed> -b <b.bed>
+
+Options: 
+	-w	Base pairs added upstream and downstream of each entry
+		in A when searching for overlaps in B.
+		- Creates symterical "windows" around A.
+		- Default is 1000 bp.
+		- (INTEGER)
+
+	-l	Base pairs added upstream (left of) of each entry
+		in A when searching for overlaps in B.
+		- Allows one to define assymterical "windows".
+		- Default is 1000 bp.
+		- (INTEGER)
+
+	-r	Base pairs added downstream (right of) of each entry
+		in A when searching for overlaps in B.
+		- Allows one to define assymterical "windows".
+		- Default is 1000 bp.
+		- (INTEGER)
+
+	-sw	Define -l and -r based on strand.  For example if used, -l 500
+		for a negative-stranded feature will add 500 bp downstream.
+		- Default = disabled.
+
+	-sm	Only report hits in B that overlap A on the same strand.
+		- By default, overlaps are reported without respect to strand.
+
+	-u	Write the original A entry _once_ if _any_ overlaps found in B.
+		- In other words, just report the fact >=1 hit was found.
+
+	-c	For each entry in A, report the number of overlaps with B.
+		- Reports 0 for A entries that have no overlap with B.
+		- Overlaps restricted by -f.
+
+	-v	Only report those entries in A that have _no overlaps_ with B.
+		- Similar to "grep -v."
+
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delta 3834
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diff --git a/obj/pairToPairMain.o b/obj/pairToPairMain.o
index f5926ff63578185fc7a639ecd9d6426b4efbf75d..995e8a0d167962a2bb06116fb709596a9ac01a33 100644
GIT binary patch
delta 2003
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delta 2009
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diff --git a/obj/shuffleBedMain.o b/obj/shuffleBedMain.o
index f1f5a4328262e8b0a6dcc22670b4704fa446a4e8..d500a8a90f8b845b6c203dfef9e463309e06d93b 100644
GIT binary patch
delta 772
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F^ATOSV7~wW

delta 781
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diff --git a/obj/slopBedMain.o b/obj/slopBedMain.o
index 804665ef5e358dd66e4b1574b7fac72c9d21a714..f1632d684aafe37e61b8fc9c0e7334ff30a3d36e 100644
GIT binary patch
delta 1022
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delta 1078
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diff --git a/src/coverageBed/coverageMain.cpp b/src/coverageBed/coverageMain.cpp
index 81b6f230..4ae9c55e 100755
--- a/src/coverageBed/coverageMain.cpp
+++ b/src/coverageBed/coverageMain.cpp
@@ -99,7 +99,7 @@ void ShowHelp(void) {
 	cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
 	
 	cerr << "Summary: Returns the depth and breadth of coverage of features from A" << endl;
-	cerr << "\t\t on the intervals in B." << endl << endl;
+	cerr << "\t on the intervals in B." << endl << endl;
 	
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
 
diff --git a/src/fastaFromBed/fastaFromBedMain.cpp b/src/fastaFromBed/fastaFromBedMain.cpp
index 72c4a067..8bba3540 100755
--- a/src/fastaFromBed/fastaFromBedMain.cpp
+++ b/src/fastaFromBed/fastaFromBedMain.cpp
@@ -112,9 +112,9 @@ void ShowHelp(void) {
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -fi -bed -fo " << endl << endl;
 
 	cerr << "Options: " << endl;
-	cerr << "\t-fi\t\tInput FASTA file" << endl;
+	cerr << "\t-fi\tInput FASTA file" << endl;
 	cerr << "\t-bed\tBED file of ranges to extract from -fi" << endl;
-	cerr << "\t-fo\t\tOutput FASTA file" << endl;
+	cerr << "\t-fo\tOutput FASTA file" << endl;
 	cerr << "\t-name\tUse the BED name field (#4) for the FASTA header" << endl;
 
 
diff --git a/src/genomeCoverageBed/genomeCoverageMain.cpp b/src/genomeCoverageBed/genomeCoverageMain.cpp
index 97f05e19..5befca26 100755
--- a/src/genomeCoverageBed/genomeCoverageMain.cpp
+++ b/src/genomeCoverageBed/genomeCoverageMain.cpp
@@ -114,12 +114,12 @@ void ShowHelp(void) {
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed> -g <genome>" << endl << endl;
 	
 	cerr << "Options: " << endl;
-	cerr << "\t-d\t\t"	     	<< "Report the depth at each genome position." << endl;
-	cerr 						<< "\t\t\tDefault behavior is to report a histogram." << endl << endl;
+	cerr << "\t-d\t"	     	<< "Report the depth at each genome position." << endl;
+	cerr 						<< "\t\tDefault behavior is to report a histogram." << endl << endl;
 
 	cerr << "\t-max\t"          << "Combine all positions with a depth >= max into" << endl;
-	cerr						<< "\t\t\ta single bin in the histogram." << endl;
-	cerr						<< "\t\t\t- (INTEGER)" << endl << endl;
+	cerr						<< "\t\ta single bin in the histogram." << endl;
+	cerr						<< "\t\t- (INTEGER)" << endl << endl;
 
 	cerr << "Notes: " << endl;
 	cerr << "\t(1)  The genome file should tab delimited and structured as follows:" << endl;
diff --git a/src/intersectBed/a.bed b/src/intersectBed/a.bed
index c7f1f6fe..dfac4d8a 100644
--- a/src/intersectBed/a.bed
+++ b/src/intersectBed/a.bed
@@ -1 +1,2 @@
+# stuff
 chr1	0	12000	a	1	+
diff --git a/src/intersectBed/b.bed b/src/intersectBed/b.bed
index 5dd93bce..74448bed 100644
--- a/src/intersectBed/b.bed
+++ b/src/intersectBed/b.bed
@@ -1 +1 @@
-chr1	50	150	b	2	-	same	to 	you
+chr1	50	150	b	2	-
diff --git a/src/linksBed/linksMain.cpp b/src/linksBed/linksMain.cpp
index 3b244344..267f8aeb 100755
--- a/src/linksBed/linksMain.cpp
+++ b/src/linksBed/linksMain.cpp
@@ -107,13 +107,13 @@ void ShowHelp(void) {
 	cerr << "Options: " << endl;
 	cerr << "\t-base\t"	<< "The browser basename.  Default: http://genome.ucsc.edu " << endl;
 	cerr << "\t-org\t"	<< "The organism. Default: human" << endl;
-	cerr << "\t-db\t\t"	<< "The build.  Default: hg18" << endl << endl;
+	cerr << "\t-db\t"	<< "The build.  Default: hg18" << endl << endl;
 	
 	cerr << "Example: " << endl;
-	cerr << "\t" << "By default, the links created will point to the human (hg18) UCSC browser." << endl;
+	cerr << "\t" << "By default, the links created will point to human (hg18) UCSC browser." << endl;
 	cerr << 		"\tIf you have a local mirror, you can override this behavior by supplying" << endl;
 	cerr <<			"\tthe -base, -org, and -db options."  << endl << endl;
-	cerr << "\t" << "For example, if the main URL of your local mirror for mouse MM9 is called: " << endl;
+	cerr << "\t" << "For example, if the URL of your local mirror for mouse MM9 is called: " << endl;
 	cerr << 		"\thttp://mymirror.myuniversity.edu, then you would use the following:" << endl;
 	cerr << 		"\t" << "-base http://mymirror.myuniversity.edu" << endl;
 	cerr << 		"\t" << "-org mouse" << endl; 
diff --git a/src/maskFastaFromBed/maskFastaFromBedMain.cpp b/src/maskFastaFromBed/maskFastaFromBedMain.cpp
index 8002f3d7..462dcf73 100755
--- a/src/maskFastaFromBed/maskFastaFromBedMain.cpp
+++ b/src/maskFastaFromBed/maskFastaFromBedMain.cpp
@@ -114,11 +114,11 @@ void ShowHelp(void) {
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -fi -out -bed" << endl << endl;
 
 	cerr << "Options:" << endl;
-	cerr << "\t-fi\t\tInput FASTA file" << endl;
+	cerr << "\t-fi\tInput FASTA file" << endl;
 	cerr << "\t-bed\tBED file of ranges to mask in -fi" << endl;
-	cerr << "\t-fo\t\tOutput FASTA file" << endl;
+	cerr << "\t-fo\tOutput FASTA file" << endl;
 	cerr << "\t-soft\tEnforce \"soft\" masking.  That is, instead of masking with Ns," << endl;
-	cerr << "\t\t\tmask with lower-case bases." << endl;
+	cerr << "\t\tmask with lower-case bases." << endl;
 
 	// end the program here
 	exit(1);
diff --git a/src/pairToBed/pairToBedMain.cpp b/src/pairToBed/pairToBedMain.cpp
index 950edced..36d7a087 100755
--- a/src/pairToBed/pairToBedMain.cpp
+++ b/src/pairToBed/pairToBedMain.cpp
@@ -176,11 +176,11 @@ void ShowHelp(void) {
 	cerr								<< "\t\tispan\tReport overlaps between [end1, start2] of A and B." << endl; 
 	cerr									<< "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl;
 	cerr								<< "\t\tospan\tReport overlaps between [start1, end2] of A and B." << endl; 
-	cerr									<< "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
-	cerr								<< "\t\tnotispan\tReport A if ispan of A doesn't overlap B." << endl; 
 	cerr									<< "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl;
+	cerr								<< "\t\tnotispan\tReport A if ispan of A doesn't overlap B." << endl; 
+	cerr									<< "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl;
 	cerr								<< "\t\tnotospan\tReport A if ospan of A doesn't overlap B." << endl; 
-	cerr									<< "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
+	cerr									<< "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
 		
 	cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl;
 
diff --git a/src/pairToPair/pairToPairMain.cpp b/src/pairToPair/pairToPairMain.cpp
index 400ec04c..8bd9e338 100755
--- a/src/pairToPair/pairToPairMain.cpp
+++ b/src/pairToPair/pairToPairMain.cpp
@@ -135,11 +135,11 @@ void ShowHelp(void) {
 	cerr << "\t-f\t"	    			<< "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
 	cerr 								<< "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
 
-	cerr << "\t-type \t"				<< "Approach to reporting overlaps between A and B." << endl;
-	cerr 								<< "\t\tneither\t\tReport overlaps if neither end of A overlaps B." << endl << endl;
+	cerr << "\t-type \t"				<< "Approach to reporting overlaps between A and B." << endl << endl;
+	cerr 								<< "\t\tneither\tReport overlaps if neither end of A overlaps B." << endl;
 
-	cerr 								<< "\t\tboth\t\tReport overlaps if both ends of A overlap B." << endl;
-	cerr									<< "\t\t\t\t- Default." << endl;
+	cerr 								<< "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
+	cerr									<< "\t\t\t- Default." << endl << endl;
 
 	cerr << "\t-is\t"	    			<< "Ignore strands when searching for overlaps." << endl;
 	cerr 								<< "\t\t- By default, strands are enforced." << endl << endl;
diff --git a/src/shuffleBed/shuffleBedMain.cpp b/src/shuffleBed/shuffleBedMain.cpp
index 004a19cb..bed823d5 100755
--- a/src/shuffleBed/shuffleBedMain.cpp
+++ b/src/shuffleBed/shuffleBedMain.cpp
@@ -119,14 +119,14 @@ void ShowHelp(void) {
 	
 	cerr << "Options: " << endl;
 	cerr << "\t-excl\t"           	<< "A BED file of coordinates in which features in -i" << endl;
-	cerr							<< "\t\t\tshould not be placed (e.g. gaps.bed)." << endl << endl;
+	cerr							<< "\t\tshould not be placed (e.g. gaps.bed)." << endl << endl;
 
 	cerr << "\t-chrom\t"      		<< "Keep features in -i on the same chromosome."<< endl; 
-	cerr							<< "\t\t\t- By default, the chrom and position are randomly chosen." << endl << endl;
+	cerr							<< "\t\t- By default, the chrom and position are randomly chosen." << endl << endl;
 
 	cerr << "\t-seed\t"     		<< "Supply an integer seed for the shuffling." << endl; 
-	cerr							<< "\t\t\t- By default, the seed is chosen automatically." << endl;
-	cerr							<< "\t\t\t- (INTEGER)" << endl << endl;
+	cerr							<< "\t\t- By default, the seed is chosen automatically." << endl;
+	cerr							<< "\t\t- (INTEGER)" << endl << endl;
 
 
 	cerr << "Notes: " << endl;
diff --git a/src/slopBed/slopBedMain.cpp b/src/slopBed/slopBedMain.cpp
index 4d162372..4504d28a 100755
--- a/src/slopBed/slopBedMain.cpp
+++ b/src/slopBed/slopBedMain.cpp
@@ -138,7 +138,7 @@ void ShowHelp(void) {
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed> -g <genome> [-b <int> or (-l and -r)]" << endl << endl;
 	
 	cerr << "Options: " << endl;
-	cerr << "\t-b\t"            	<< "Increase the BED entry by the same number base pairs in each direction." << endl;
+	cerr << "\t-b\t"            	<< "Increase the BED entry by -b base pairs in each direction." << endl;
 	cerr 							<< "\t\t- (Integer)" << endl;
 		
 	cerr << "\t-l\t"            	<< "The number of base pairs to subtract from the start coordinate." << endl;
@@ -152,12 +152,12 @@ void ShowHelp(void) {
 	cerr							<< "\t\tit will add 500 bp downstream.  Default = false." << endl << endl;	
 
 	cerr << "Notes: " << endl;
-	cerr << "\t(1)  Starts will be set to 0 if the requested slop would force it below 0." << endl;
-	cerr << "\t(2)  Ends will be set to the chromosome length if the requested slop would" << endl;
-	cerr <<	       "\t\t force it above the max chrom length." << endl;
+	cerr << "\t(1)  Starts will be set to 0 if options would force it below 0." << endl;
+	cerr << "\t(2)  Ends will be set to the chromosome length if  requested slop would" << endl;
+	cerr <<	       "\tforce it above the max chrom length." << endl;
 
 	cerr << "\t(3)  The genome file should tab delimited and structured as follows:" << endl;
-	cerr << "\t     <chromName><TAB><chromSize>" << endl << endl;
+	cerr << "\n\t<chromName><TAB><chromSize>" << endl << endl;
 	cerr << "\tFor example, Human (hg19):" << endl;
 	cerr << "\tchr1\t249250621" << endl;
 	cerr << "\tchr2\t243199373" << endl;
-- 
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