bamranksort - sort BAM files by rank
bamranksort [options]
bamranksort reads a BAM file (preferably in nearly sorted order), sorts
it in rank order and then outputs a BAM.
The input BAM file must already have the rank prefix added to the alignment
names and any attempt to sort a file without these name prefixes will fail.
bamranksort also assumes that all alignments of the same name are
grouped together (a pair of reads plus any number of supplementary/secondary
reads). If it finds any alignments in a separate group the program will exit.
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=<0|1|2>: Valid values are
- 0:
- do not print progress report (default).
- 1:
- print progress report to standard error.
- 2:
- print more values for debugging only to standard
error.
md5=<0|1>: md5 checksum creation for output file. This option can
only be given if outputformat=bam. Then 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.
misordered=<500000>: number of alignments to accumulate before
giving up.
step=<2>: expected increment between ranks.
outputthreads=<[1]>: output helper threads.
Written by Andrew Whitwham.
Report bugs to <
[email protected]>
Copyright © 2015 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.