.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH WHAM-BUILD "1" "February 2021" "wham-build 0.1.5" "User Commands"
.SH NAME
wham-build \- Wisconsin's High-Throughput Alignment Method
.SH DESCRIPTION
.SS "Usage:"
.IP
wham\-build [options]* \fB\-l\fR <int> <ref_sequence> <basepath>
\fB\-l\fR <int>         specify the length of short reads
<ref_sequence>   comma\-separated list of fiels with ref sequences
<basepath>       write wham data to files with this dir/basename
.SH OPTIONS
.TP
\fB\-v\fR <int>
report hits with <=v errors (0\-5), ignore qualities
.TP
\fB\-p\fR <int>
specify the number of fragments for alignments
.TP
\fB\-m\fR <int>
discard subsequences appearing more than <int> times (default: 100).
.TP
\fB\-b\fR <int>
specify the number of buckets
.TP
\fB\-a\fR
find all valid matches (need much more memory)
.TP
\fB\-\-mask\fR
keep masked characters in the sequences (default: on)
.TP
\fB\-\-unmask\fR
discard masked characters in the sequences. Masks are treated as Ns
.TP
\fB\-\-version\fR
print version information
.TP
\fB\-h\fR/\-\-help
print this usage message
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.