NAME

       abyss-fixmate - Fill the paired-end fields of SAM alignments

SYNOPSIS

       abyss-fixmate [OPTION]... [FILE]...

DESCRIPTION

       Write  read pairs that map to the same contig to the file SAME.  Write read pairs that map
       to different contigs to stdout.  Alignments may be in FILE(s) or standard input.

              Options:

       --no-qname
              set the qname to * [default]

       --qname
              do not alter the qname

       --all  print all alignments

       --diff print alignments that align to different contigs [default]

       -l, --min-align=N
              the minimal alignment size [1]

       -s, --same=SAME
              write properly-paired reads to this file

       -h, --hist=FILE
              write the fragment size histogram to FILE

       -c, --cov=FILE
              write the physical coverage to FILE

       -v, --verbose
              display verbose output

       --help display this help and exit

       --version
              output version information and exit

       --db=FILE
              specify path of database repository in FILE

       --library=NAME
              specify library NAME for sqlite

       --strain=NAME
              specify strain NAME for sqlite

       --species=NAME
              specify species NAME for sqlite

AUTHOR

       Written by Shaun Jackman.

REPORTING BUGS

       Report bugs to <abyss-users@bcgsc.ca>.

COPYRIGHT

       Copyright 2014 Canada's Michael Smith Genome Sciences Centre