bambisect1
Find reduced size bam file on which a program fails
Usage
bambisect [options]
in.bam
prog
Overview
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
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).