bamchecksort - check sort order of a BAM file

       Written by German Tischler.

       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.

BIOBAMBAM                                         October 2013                                   BAMCHECKSORT(1)

       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

       bamchecksort - check sort order of a BAM file

       Report bugs to <germant@miltenyibiotec.de>

bamchecksort [options]