diff --git a/bin/coverageBed b/bin/coverageBed
index eee6e34538a4a9bf4697f901c0cc8b386749b7b9..0b0692ca1097bdf6f07e74841ef53dbb8ea46f21 100755
Binary files a/bin/coverageBed and b/bin/coverageBed differ
diff --git a/bin/fastaFromBed b/bin/fastaFromBed
index 7063e23e96e2e06d91285bf59b473cac583c2ace..be388680a3e541caa9ffb03ff17fd4db3c7cff7f 100755
Binary files a/bin/fastaFromBed and b/bin/fastaFromBed differ
diff --git a/bin/genomeCoverageBed b/bin/genomeCoverageBed
index d597ce6e93355c1a5f8eb2ca51c7b4d55af0f5dc..cc39fb5ceb10d1772e10fa76cc5e3192ecd9acc6 100755
Binary files a/bin/genomeCoverageBed and b/bin/genomeCoverageBed differ
diff --git a/bin/linksBed b/bin/linksBed
index 3430a144ad06c4cd6be62be00f51b3c7b62a63de..d8964988051cdc4fe281417da3e7ec93f59690d0 100755
Binary files a/bin/linksBed and b/bin/linksBed differ
diff --git a/bin/maskFastaFromBed b/bin/maskFastaFromBed
index 90cb6dbed12aef22eddbe8fe67f7f3d999e1806a..83b1d0e4249e288c250108a4a8f14220648de49e 100755
Binary files a/bin/maskFastaFromBed and b/bin/maskFastaFromBed differ
diff --git a/bin/pairToBed b/bin/pairToBed
index c5a4f41d66812e3aa97ebd6d203f9169336a464c..bd19f8e101c232886d7a99e4388c700748516384 100755
Binary files a/bin/pairToBed and b/bin/pairToBed differ
diff --git a/bin/pairToPair b/bin/pairToPair
index c50b5e5122e7e52b11e2476cb160654a2ae3b4ed..3a2ede01fae21d0f18f07aadb92f5de4467dcd30 100755
Binary files a/bin/pairToPair and b/bin/pairToPair differ
diff --git a/bin/shuffleBed b/bin/shuffleBed
index 759bf6205863981d56b0e9820d4a0912e786a8dd..d990a9e0f33bf81f771f3c6aeafde765344f26c6 100755
Binary files a/bin/shuffleBed and b/bin/shuffleBed differ
diff --git a/bin/slopBed b/bin/slopBed
index 69ad500cd13b64b64b4500c4630afae8ee1e4a0c..4ab09549b1320598f56f7f089ecb61cddf9c6cbc 100755
Binary files a/bin/slopBed and b/bin/slopBed differ
diff --git a/genomes/mouse.mm8.genome b/genomes/mouse.mm8.genome
new file mode 100644
index 0000000000000000000000000000000000000000..904ce1ebf294f37c539238eebfc7d76d2effa1a6
--- /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 0000000000000000000000000000000000000000..84c1e72431d01f38c38346d7df191c1eefe0aa48
--- /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 0000000000000000000000000000000000000000..869778141609467030385afb7bd3ed625f6957f9
--- /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."
+
diff --git a/obj/coverageMain.o b/obj/coverageMain.o
index 3c9d29313fecb8571879892c04cee1fa6d346348..ff623f9b5c224c75bbaeb7b932bbc8cd9a9162c2 100644
Binary files a/obj/coverageMain.o and b/obj/coverageMain.o differ
diff --git a/obj/fastaFromBedMain.o b/obj/fastaFromBedMain.o
index c6b694112889ecbc30f2254a4c95c5fcd029983b..333edb984e44be765db87892ac223cdc2a1733cf 100644
Binary files a/obj/fastaFromBedMain.o and b/obj/fastaFromBedMain.o differ
diff --git a/obj/genomeCoverageMain.o b/obj/genomeCoverageMain.o
index 77908556aa21933ab30197d3e3be01af32c60d1d..4fce9315d3429b7958c4e208b75ba4e915b04754 100644
Binary files a/obj/genomeCoverageMain.o and b/obj/genomeCoverageMain.o differ
diff --git a/obj/linksMain.o b/obj/linksMain.o
index 37b3f6c9d40494e45d14eb5c6ab984fb67404e0e..baf191385025aad8c202b33d92bd7cc5b17ce939 100644
Binary files a/obj/linksMain.o and b/obj/linksMain.o differ
diff --git a/obj/maskFastaFromBedMain.o b/obj/maskFastaFromBedMain.o
index 838fd9c3eb1fa9c5a3f81842f085c2b878f545b7..b833137886ade820131e0a25c98e3c76abaa1aac 100644
Binary files a/obj/maskFastaFromBedMain.o and b/obj/maskFastaFromBedMain.o differ
diff --git a/obj/pairToBedMain.o b/obj/pairToBedMain.o
index 0a654380dd6c424e4421a57b5b8b628005fe1dd3..a0b90a6c0589c75e404603d9e987def433dd49d2 100644
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diff --git a/obj/pairToPairMain.o b/obj/pairToPairMain.o
index f5926ff63578185fc7a639ecd9d6426b4efbf75d..995e8a0d167962a2bb06116fb709596a9ac01a33 100644
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diff --git a/obj/shuffleBedMain.o b/obj/shuffleBedMain.o
index f1f5a4328262e8b0a6dcc22670b4704fa446a4e8..d500a8a90f8b845b6c203dfef9e463309e06d93b 100644
Binary files a/obj/shuffleBedMain.o and b/obj/shuffleBedMain.o differ
diff --git a/obj/slopBedMain.o b/obj/slopBedMain.o
index 804665ef5e358dd66e4b1574b7fac72c9d21a714..f1632d684aafe37e61b8fc9c0e7334ff30a3d36e 100644
Binary files a/obj/slopBedMain.o and b/obj/slopBedMain.o differ
diff --git a/src/coverageBed/coverageMain.cpp b/src/coverageBed/coverageMain.cpp
index 81b6f230a10acadeaae4d59483a22ed510509355..4ae9c55eeea3f0f175d4485f7ade762b20e23abd 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 72c4a0673ee6a7299bdd419646edf27149169a4f..8bba3540b755c5b887412d30df7fc1fe7f9d020f 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 97f05e1952d4c7cd9ff2df89a88933c8a9a1ac91..5befca26c8df54b38cfabde7d9d6c47f09670777 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 c7f1f6fe149868ee3e61cf8554114c5ff138aee8..dfac4d8a884e3b6defcb8a7381eb397cc6351815 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 5dd93bce889287f2550f825419776fffe9d1e662..74448bed448bbaca798cbd567b35cfa6250c830d 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 3b244344b4bbf933bb373171f04f96fb0cdd094c..267f8aeb3458925967117c8699d96d1cc22c73be 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 8002f3d7d0b0d4707c92fcd141367174a57c23a0..462dcf73ca2ee237bb9790808a0b3718ba792dc0 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 950edced4b4cbbd4af10925deb93e2b167847687..36d7a087c6f369832178a5c0d24cd1bbc12be8de 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 400ec04c71b88d74d330b96f6fc7dee36c84897d..8bd9e338d590279dfa02148c113368ffd4d3fb2d 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 004a19cb6d432de91f890edba9aa4c167d7bcad7..bed823d57a855a1dfe100ccf3ac80f91bd5ce7ee 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 4d162372e8657a1daa9ad558afad5d72bb3905fa..4504d28aa7b1f3876bda5a893b8085f1cc65db7b 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;