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.