NAME

       bamfillquery - fill query sequences into BAM files

SYNOPSIS

       bamfillquery [options] <in.bam queries.fasta >out.bam

DESCRIPTION

       bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences found in the
       FastA file into the query sequence field of the SAM/BAM/CRAM file and writes the resulting
       data  to  a SAM/BAM/CRAM file. Both the alignment input file and the FastA file need to be
       sorted by query name. See bamsort or bamsormadup for sorting the SAM/BAM/CRAM file to this
       order.

       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=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

       tmpfile=<filename>: prefix for temporary files. By default the temporary files are created
       in the current directory

       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.

       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:

       bam:   BAM (see http://samtools.sourceforge.net/SAM1.pdf)

       sam:   SAM (see http://samtools.sourceforge.net/SAM1.pdf)

       cram:  CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit)

       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:

       bam:   BAM (see http://samtools.sourceforge.net/SAM1.pdf)

       sam:   SAM (see http://samtools.sourceforge.net/SAM1.pdf)

       cram:  CRAM  (see  http://www.ebi.ac.uk/ena/about/cram_toolkit).  This   format   is   not
              advisable for data sorted by query name.

       I=<[stdin]>: input filename, standard input if unset.

       O=<[stdout]>: output filename, standard output if unset.

       inputthreads=<[1]>: input helper threads, only valid for inputformat=bam.

       outputthreads=<[1]>: output helper threads, only valid for outputformat=bam.

       reference=<[]>:  reference FastA file for inputformat=cram and outputformat=cram. An index
       file (.fai) is required.

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <germant@miltenyibiotec.de>

COPYRIGHT

       Copyright © 2009-2016 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.