.TH BAMAUXMERGE 1 "July 2013" BIOBAMBAM
.SH NAME
bamauxmerge - merge information in unmapped and mapped alignment files
.SH SYNOPSIS
.PP
.B bamauxmerge
[options]
in_unmapped in_mapped
.SH DESCRIPTION
bamauxmerge reads and merges two SAM/BAM/CRAM files which are expected to have the
following properties:

.IP *
the first file contains only unmapped reads and it's header contains no SQ lines

.IP *
the second file was produced by an aligner based on the content of the first file.

.IP *
the order of the reads is the same in the first an second file
into a single alignment file.
.PP
The headers of the two files are merged in the following file:

.IP *
the SQ lines contained in the header of the second file are appended to the header of the first file to obtain the header of the output file

.IP *
all other header information from the second file is discarded
.PP
The output records are constructed in the following way:

.IP 1.
Take a record from the second file

.IP 2.
Copy all aux fields from the corresponding record in the first file which are not already present.

.PP
The following key=value pairs can be given:
.PP
.B level=<-1|0|1|9|11>:
set compression level of the output BAM file. Valid
values are
.IP -1:
zlib/gzip default compression level
.IP 0:
uncompressed
.IP 1:
zlib/gzip level 1 (fast) compression
.IP 9:
zlib/gzip level 9 (best) compression
.P
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
.IP 11:
igzip compression
.PP
.B verbose=<1>:
Valid values are
.IP 1:
print progress report on standard error
.IP 0:
do not print progress report
.PP
.B tmpfile=<filename>: 
prefix for temporary files. By default the temporary files are created in the current directory
.PP
.B md5=<0|1>:
md5 checksum creation for output file. Valid values are
.IP 0:
do not compute checksum. This is the default.
.IP 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.
.PP
.B md5filename
file name for md5 checksum if md5=1.
.PP
.B index=<0|1>:
compute BAM index for output file. Valid values are
.IP 0:
do not compute BAM index. This is the default.
.IP 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.
.PP
.B indexfilename
file name for BAM index if index=1.
.PP
.B inputformat=<bam>: input file format.
All versions of bamsort come with support for the BAM input format. If
the program in addition is linked to the io_lib package, then the following
options are valid:
.IP bam:
BAM (see http://samtools.sourceforge.net/SAM1.pdf)
.IP sam:
SAM (see http://samtools.sourceforge.net/SAM1.pdf)
.IP cram:
CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit)
.PP
.B outputformat=<bam>: output file format.
All versions of bamsort come with support for the BAM output format. If
the program in addition is linked to the io_lib package, then the following
options are valid:
.IP bam:
BAM (see http://samtools.sourceforge.net/SAM1.pdf)
.IP sam:
SAM (see http://samtools.sourceforge.net/SAM1.pdf)
.IP cram:
CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit). This format is not advisable for data sorted by query name.
.PP
.B inputthreads=<[1]>:
input helper threads, only valid for inputformat=bam.
.PP
.B outputthreads=<[1]>:
output helper threads, only valid for outputformat=bam.
.SH AUTHOR
Written by German Tischler.
.SH "REPORTING BUGS"
Report bugs to <germant@miltenyibiotec.de>
.SH COPYRIGHT
Copyright \(co 2009-2013 German Tischler, \(co 2011-2013 Genome Research Limited.
License GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>
.br
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.