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.

BIOBAMBAM                                           July 2019                                       BAMBISECT(1)