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.