NAME

       bamcollate - collate reads in a BAM file by name

SYNOPSIS

       bamcollate [options]

DESCRIPTION

       Please  note:  This  program is deprecated. Please use bamcollate2 instead.  bamcollate is
       only present for compatibility reasons with older scripts.

       bamcollate reads a BAM file from standard input, collates the  contained  reads/alignments
       by name and writes the resulting data to standard output in BAM format.

       The following key=value pairs can be given:

       tmpfile=<filename>  file name of temporary file used for collation. By default a temporary
       file is created in the current directory.

       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

       colhashbits=<20> base two logarithm of the size of the hash table used for collation  (the
       default value is 20 and should work reasonably well for most input files)

       collistsize=<524288>  size  of hash table overflow list in alignments (the default is 512k
       and should work reasonably well for most input files)

       pairsonly=<0|1>: output pairs only. Valid values are

       0:     output all alignments

       1:     output pairs only (no unmatched/orphans)

       readgroups=<>: output only reads/alignments in the given list  of  read  groups.  Multiple
       read  groups  are  given  separated  by comma. No filtering is performed if the key is not
       given.

       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.

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <tischler@mpi-cbg.de>

COPYRIGHT

       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.