NAME

       bambisect - find reduced size BAM file on which a program fails

SYNOPSIS

       bambisect [options] in.bam prog

DESCRIPTION

       bambisect  runs  prog on in.bam. If this fails (signified by a non-zero return code), then
       it systematically reduces the number of records by extracting intervals  of  records  from
       in.bam and rerunning prog on such intervals until it finds an interval on which prog fails
       but succeeeds on any proper sub interval.

       The following key=value pairs can be given:

       level=<-1|0|1|9>: set compression level used when compressing BAM. Valid values are values
       are

       -1:    zlib/gzip default compression level

       0:     uncompressed

       1:     zlib/gzip level 1 (fast) compression

       9:     zlib/gzip level 9 (best) compression

       verbose=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

       tmpfile=<filename>: prefix for temporary files. By default the temporary files are created
       in the current directory

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <germant@miltenyibiotec.de>

COPYRIGHT

       Copyright © 2009-2019 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.