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.