NAME¶

bamranksort - sort BAM files by rank

SYNOPSIS¶

bamranksort [options]

DESCRIPTION¶

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.

AUTHOR¶

Written by Andrew Whitwham.

REPORTING BUGS¶

Report bugs to <aw7@sanger.ac.uk>

COPYRIGHT¶

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.