Usage: bwcat -i input-path

-i  --input-path [file]    Path to the input bigwig file

Optional:
-r  --region [string]      Region or bw file to print to screen format. NB start should be 0 based: (contig:start-stop)
-n  --include-na           Include NA regions in output
-o  --output [file]        File to write bw output to [default: stdout]

Other:
-h --help                  Display this usage information.
-v --version               Prints the version number.

Usage: bwjoin -f genome.fai -o output.bw

-p  --input-path [dir]                           Path to the input bigwig files named [path]/<contig_name>.bw
-f  --fasta-index [file]                         Fasta index file (.fai)
-o  --outfile [file]                             Path to the output .bw file produced. [default:'concatenated.bw']
-g  --ignore-contigs [comma separated list]      Comma separated list of contigs to ignore.

Other:
-h --help      Display this usage information.
-v --version   Prints the version number.

Usage: bam2bw -i input.[b|cr]am -o output.bw
bam2bw can be used to generate a bw file of coverage from a [cr|b]am file.

-i  --input [file]                                Path to the input [b|cr]am file.
-F  --filter [int]                                SAM flags to filter. [default: 4]
-f  --filter-include [int]                        SAM flags to include. [default: 0]
                                                  N.B. if properly paired reads are filtered for inclusion bam2bw will assume paired-end data
                                                  and exclude any proper-pair flagged reads not in F/R orientation.-o  --outfile [file]                              Path to the output .bw file produced. [default:'output.bam.bw']

Optional:
-S  --scale-log10 [float]                         A scale factor to multiply to output [default: -1912244352]
-c  --region [file]                               A samtools style region (contig:start-stop) or a bed file of regions over which to produce the bigwig file
-z  --include-zeroes                              Include zero coverage regions as additional entries to the bw file
-r  --reference [file]                            Path to reference genome.fa file (required for cram if ref_path cannot be resolved)
-a  --overlap                                     Use overlapping read check

Other:
-h  --help                                        Display this usage information.
-v  --version                                     Prints the version number.

Usage: bg2bw -i input.bed -c chrom.list -o output.bw
bg2bw can be used to generate a bw file from a bedgraph file.

-i  --input [file]           Path to the input [b|cr]am file.
-o  --outfile [file]         Path to the output .bw file produced. [default:'output.bw']
-c  --chromList [file]       Path to chrom.list a .tsv where first two columns are contig name and length.

Other:
-h  --help                   Display this usage information.
-v  --version                Prints the version number.

Usage: bam2bwbases -i input.[b|cr]am -o output.bw
bam2bwbases can be used to generate four bw files of per base proportions.

-i  --input [file]                                Path to the input [b|cr]am file.
-F  --filter [int]                                SAM flags to filter. [default: 4]
-o  --outfile [file]                              Path to the output .bw file produced. Per base results wiillbe output as four bw files [ACGT].outputname.bw [default:'(null)']
-a  --overlap                                     Turn on overlaping reads check

Optional:
-c  --region [file]                               A samtools style region (contig:start-stop) or a bed file of regions over which to produce the bigwig file
-r  --reference [file]                            Path to reference genome.fa file (required for cram if ref_path cannot be resolved)

Other:
-h  --help                                        Display this usage information.
-v  --version                                     Prints the version number.

Usage: bam2bedgraph -i input.[cr|b]am -o file [-r region] [-h] [-v]

Create a BEDGraph file of genomic coverage. BAM file must be sorted.
-i --input     Path to bam/cram input file. [default: stdin]
-o --output    File path for output. [default: stdout]

Optional:
-r --region    Region in bam to access.
-f --filter    Ignore reads with the filter flags [int].
-a --overlap  Turn on overlaping reads check

Other:
-h --help      Display this usage information.
-v --version   Prints the version number.

Copyright (c) 2017-2018 Genome Research Ltd.

Author: David Jones <cgphelp@sanger.ac.uk>

This file is part of cgpBigWig.

cgpBigWig is free software: you can redistribute it and/or modify it under
the terms of the GNU Affero General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option) any
later version.

This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
details.

You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.

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including the first and last year specified and all consecutive years between
them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
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