bamrank - insert the rank (line number) of each alignment as an auxiliary field
for tag zz
bamrank [options]
bamrank reads a BAM file from standard input, inserts a new auxiliary field
tagged zz containing the rank (line number) of the respective read/alignment
and writes the resulting data to standard output as a BAM file. This rank can
be used to restore the original order of the file after reordering by using
the sequence
bamzztoname | bamsort SO=queryname | bam12strip
The following key=value pairs can be given:
level=<-1|0|1|9|11>: set compression level of the output BAM file.
Valid values are
- -1:
- zlib/gzip default compression level
- 0:
- uncompressed
- 1:
- zlib/gzip level 1 (fast) compression
- 9:
- zlib/gzip level 9 (best) compression
If libmaus has been compiled with support for igzip (see
https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data)
then an additional valid value is
- 11:
- igzip 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
md5=<0|1>: md5 checksum creation for output file. Valid values are
- 0:
- do not compute checksum. This is the default.
- 1:
- compute checksum. If the md5filename key is set, then the
checksum is written to the given file. If md5filename is unset, then no
checksum will be computed.
md5filename file name for md5 checksum if md5=1.
index=<0|1>: compute BAM index for output file. Valid values are
- 0:
- do not compute BAM index. This is the default.
- 1:
- compute BAM index. If the indexfilename key is set, then
the BAM index is written to the given file. If indexfilename is unset,
then no BAM index will be computed.
indexfilename file name for BAM index if index=1.
Written by German Tischler.
Report bugs to <
[email protected]>
Copyright © 2009-2013 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.