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