Command line option formatting standardized.

genomes/mouse.mm8.genome

+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
+

genomes/mouse.mm9.genome

+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
+

log

+
+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."
+