NAME¶

SYNOPSIS¶

DESCRIPTION¶

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¶

REPORTING BUGS¶

COPYRIGHT¶