NAME

       bamauxmerge2 - merge information in unmapped and mapped BAM files

SYNOPSIS

       bamauxmerge2 [options] in_unmapped in_mapped

DESCRIPTION

       bamauxmerge2  reads  and  merges  two  BAM  files which are expected to have the following
       properties

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

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

       *      both files are sorted in query name order into a single alignment file.

       The headers of the two files are merged in the following file:

       *      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

       *      all other header information from the second file is discarded

       The output records are constructed in the following way:

       1.     Take a record from the second file

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

       3.     Reinsert clipped adapter bases/quality values stored in the qs/qq by aux fields  by
              fastqtobam2  and  remove  the  qs/qq  aux  fields  while inserting appropriate soft
              clipping CIGAR operations.

       4.     Fix mate information like bamfixmateinformation.

       5.     Insert the mate CIGAR information fields MC and MS if the mate is aligned.

       6.     Insert the MQ (mate quality) aux field.

       The following key=value pairs can be given:

       zz=<0|1>: replace read name by content of nn aux field. Valid values are

       1:     replace read name

       0:     do not replace read name

       calmdnm=<0|1>: recompute MD and NM aux fields. Valid values are

       1:     recompute MD and NM aux fields. This requires the calmdnmreference key to be set to
              the name of an appropriate FastA file.

       0:     do not recompute MD and NM aux fields

       calmdnmreference=<>: reference FastA file.

       replacecigar=<0|1>:  replace  M  cigar  operations  by the appropriate = and X operations.
       Valid values are

       1:     replace cigar operations. This requires the  calmdnmreference  key  to  be  set  on
              invocation.

       0:     do not replace cigar operations

       hash=<crc32prod>: hash used for computing sequence checksums. See bamseqchksum for further
       information.

       filehash=<md5>: hash used for computing output file checksums.

       chksumfn=<>: file name used for storing sequence checksum  information.  By  default  this
       information is not saved.

       filehashfn=<>:  file  name  used  for  storing  file checksum information. By default this
       information is not saved.

       level=<-1|0|1|9>: 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

       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.

       threads=<[1]>: number of threads used for processing. By default 1 thread is used. Set  to
       0 for using as many threads as CPU cores detected.

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <germant@miltenyibiotec.de>

COPYRIGHT

       Copyright  ©  2009-2019  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.