NAME

       bamchecksort - check sort order of a BAM file

SYNOPSIS

       bamchecksort [options]

DESCRIPTION

       bamchecksort  reads a BAM file via standard input and checks the sort order of the records
       in the file.  For query name sorted files the program strictly checks the  order  used  by
       the  bamsort program, i.e. it requires reads marked as read 1 to appear before such marked
       as read 2 for lines with equal names.

       The following key=value pairs can be given:

       verbose=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <germant@miltenyibiotec.de>

COPYRIGHT

       Copyright © 2009-2013 German Tischler,  ©  2011-2013  Genome  Research  Limited.   License
       GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>
       This  is free software: you are free to change and redistribute it.  There is NO WARRANTY,
       to the extent permitted by law.