.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH WHAM "1" "February 2021" "wham 0.1.5" "User Commands"
.SH NAME
wham \- Wisconsin's High-Throughput Alignment Method
.SH DESCRIPTION
.SS "Usage:"
.IP
wham [options]* {<readfile> | \fB\-1\fR <m1file> \fB\-2\fR <m2file>} <basepath> <output>
<readfile>         comma\-separated list of files containing unpaired reads
<m1file>           comma\-separated list of files containing upstream mates
<m2file>           comma\-separated list of files containing downstream mates
<basepath>         write wham data to files with this dir/basename
<output>           file to write alignments to
.SS "Input options:"
.TP
\fB\-l\fR <int>
use first <int> bases in each read
.SS "Alignment options:"
.TP
\fB\-v\fR <int>
specify the max number of errors in a reported alignment.
.TP
\fB\-g\fR/\-\-gap <int>
specify the max number of gaps in a reported alignment.
.TP
\fB\-e\fR/\-\-maqerr <int>
max sum of mismatch quals across alignment
.TP
\fB\-\-nofw\fR/\-\-norc
do not align to forward/reverse\-complement ref strand
.TP
\fB\-\-nofr\fR/\-\-norf
do not align to mate1/mate2 strand: fw/rev, rev/fw.
.TP
\fB\-I\fR/\-\-minins <int>
minimum insert size for paired\-end alignment (default: 0).
.TP
\fB\-X\fR/\-\-maxins <int>
maximum insert size for paired\-end alignment (default: 250).
.SS "Reporting options:"
.TP
\fB\-k\fR <int>
report up to <int> valid alignemtns per read (default: 1).
.TP
\fB\-a\fR/\-\-all
report all valid alignments per read.
.TP
\fB\-\-best\fR
reprot valid alignments in a sorted order of quality.
.TP
\fB\-m\fR <int>
discard reads with more than <int> valid alignmetns.
.SS "Output options:"
.TP
\fB\-S\fR/\-\-sam
write alignment in SAM format
.TP
\fB\-\-al\fR <fname>
write aligned reads/pairs to file(s) <fname>
.TP
\fB\-\-un\fR <fname>
write unaligned reads/pairs to file(s) <fname>
.SS "Performance options:"
.TP
\fB\-t\fR <int>
specify the number of threads
.TP
\fB\-\-nocat\fR
do not concatenate results from various threads
.TP
\fB\-\-step\fR <int>
specify the number of indexes that fit into memory.
.SS "Other options:"
.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.