NAME

       fastqtobam - convert FastQ to unmapped BAM

SYNOPSIS

       fastqtobam [options]

DESCRIPTION

       fastqtobam reads one or two FastQ files and converts them to a BAM file in which each read
       is marked as unmapped. If no input file name is given, then a single FastQ  file  is  read
       from  standard input. If one file name is given, then a single FastQ file is read from the
       given file. In both cases the read names in the file are parsed to determine  whether  the
       contained  reads  are  paired or not if the name scheme is not set to pairedfiles.  If two
       file names are given, then  the  program  assumes  to  find  two  FastQ  files  which  are
       synchronous,  i.e. where the first read in the first file is the mate of the first read in
       the second file etc. Input file names can be given either via  the  I  key  or  after  the
       key=value  pairs  on  the command line. The program accepts read name formats as described
       below under the key namescheme.

       The following key=value pairs can be given:

       verbose=<[0|1]> print progress report. By default progress is not reported.

       I=<filename>: input file name (data is read from standard input  if  this  option  is  not
       given). This key can be given twice.

       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

       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.

       gz=<[0|1]> input is gzip compressed FastQ. By default input is assumed to be  uncompressed
       FastQ.

       threads=<1> additional BAM encoding helper threads.

       PGID=<>  read  group identifier for reads. By default no read group identifer is set.  The
       fields CN, DS, DT, FO, KS, LB, PG, PI, PL, PU and SM of the corresponding @RG header  line
       can be set by using the keys RGCN, RGDS, etc.  respectively.

       qualityoffset=<33> FastQ quality offset. This value is subtracted from the ASCII character
       representation to get the quality score value.

       qualitymax=<41> maximum valid quality value, 41 by default. Higher values may  indicate  a
       wrong setting of the qualityoffset parameter. BAM allows quality values up to the value of
       94.

       qualityhist=<0> compute a quality histogram and print it on  the  standard  error  channel
       after  processing  has finished successfully. Lines for the quality histogram are prefixed
       with [H] and contain tab separated values. The histogram enumerates  quality  scores  from
       high  to  low  values. The histogram has four columns (after the [H] marker). The first is
       the ASCII representation of the quality with offset 33, i.e. the symbol ! denotes  quality
       0.  The  second  column gives the absolute frequency of the value. The third column stores
       the relative frequency of the value, i.e. the fraction of  all  values  assigned  to  this
       value.  The fourth column gives a cumulative relative frequency value over all quality for
       the current line and those for higher quality values.

       checkquality=<1> check whether quality values are in range and  terminate  if  an  invalid
       value is encountered.

       namescheme=<generic>  read  name  scheme. This determines how read names are parsed. There
       are four possible options:

       generic:
              the first sequence of non whitespace characters is extracted from the @ line of the
              FastQ  record and the rest of the @ line is discarded. If the retained name ends in
              /1 or /2, then the read is part of a read pair, otherwise it is the single read for
              the template. For a pair the part of the name before the /1 or /2 is considered the
              template name. For a single the whole name is considered the name of the template.

       c18s:  The name is expected to consist of two  sequences  of  non  white-space  characters
              where  the  first  contains  seven colon separated fields and the second four colon
              separated fields. The first of the  two  is  considered  to  be  the  name  of  the
              template. It is assumed that this read is the only read for the template.

       c18pe: As  for  c18s,  the name is expected to consist of two sequences of non white-space
              characters where the first contains seven colon separated  fields  and  the  second
              four  colon  separated fields. The first of the two is considered to be the name of
              the template. The read is assumed to be part of a read pair. The first field in the
              second non-whitespace sequence of the @ line designates, whether it is the first or
              second of the pair depending on  whether  the  field  stores  the  number  1  or  2
              respectively.

       pairedfiles:
              The  input framgents are assumed to be paired. If there is a single input file then
              the pairs are expected consecutive in the file. If there are two input  files  then
              the  read  names in the two are expected to be synchronous.  All characters in read
              names beginning from the first white space character are discarded. If the two  (so
              reduced)  read names in question end on /1 and /2 respectively, then those suffixes
              will be clipped off also. The remaining read names are  checked  for  equality.  If
              they are not equal, then the program will reject the input and terminate.

AUTHOR

       Written by German Tischler.

REPORTING BUGS

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

COPYRIGHT

       Copyright  ©  2009-2014  German  Tischler,  ©  2011-2014 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.