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.