wham - Wisconsin's High-Throughput Alignment Method

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

wham 0.1.5                                        February 2021                                          WHAM(1)

Usage:
              wham   [options]*   {<readfile>   |  -1  <m1file>  -2  <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

   Inputoptions:-l <int>
              use first <int> bases in each read

   Alignmentoptions:-v <int>
              specify the max number of errors in a reported alignment.

       -g/--gap <int>
              specify the max number of gaps in a reported alignment.

       -e/--maqerr <int>
              max sum of mismatch quals across alignment

       --nofw/--norc
              do not align to forward/reverse-complement ref strand

       --nofr/--norf
              do not align to mate1/mate2 strand: fw/rev, rev/fw.

       -I/--minins <int>
              minimum insert size for paired-end alignment (default: 0).

       -X/--maxins <int>
              maximum insert size for paired-end alignment (default: 250).

   Reportingoptions:-k <int>
              report up to <int> valid alignemtns per read (default: 1).

       -a/--all
              report all valid alignments per read.

       --best reprot valid alignments in a sorted order of quality.

       -m <int>
              discard reads with more than <int> valid alignmetns.

   Outputoptions:-S/--sam
              write alignment in SAM format

       --al <fname>
              write aligned reads/pairs to file(s) <fname>

       --un <fname>
              write unaligned reads/pairs to file(s) <fname>

   Performanceoptions:-t <int>
              specify the number of threads

       --nocat
              do not concatenate results from various threads

       --step <int>
              specify the number of indexes that fit into memory.

   Otheroptions:--version
              print version information

       -h/--help
              print this usage message

       wham - Wisconsin's High-Throughput Alignment Method