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.

BIOBAMBAM                                           May 2015                                      BAMRANKSORT(1)