|BAMBISECT(1)||General Commands Manual||BAMBISECT(1)|
bambisect - find reduced size BAM file on which a program fails
bambisect [options] in.bam prog
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
- zlib/gzip default compression level
- zlib/gzip level 1 (fast) compression
- zlib/gzip level 9 (best) compression
verbose=<1>: Valid values are
- print progress report on standard error
- do not print progress report
tmpfile=<filename>: prefix for temporary files. By default the temporary files are created in the current directory
Written by German Tischler.
Report bugs to <firstname.lastname@example.org>
Copyright © 2009-2019 German Tischler, © 2011-2013
Genome Research Limited. License GPLv3+: GNU GPL version 3
This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.