xenial (1) DBshow.1.gz

Provided by: dazzdb_1.0-1_amd64 bug

NAME

       DBshow - display reads stored in a Dazzler database

SYNOPSIS

       DBshow [-unqUQ] [-wint(80)] [-mtrack]+ path:db|dam [ reads:FILE | reads:range ...  ]

DESCRIPTION

       Displays  the requested reads in the database path.db or path.dam.  By default the command applies to the
       trimmed database, but if -u is set then the entire DB is used.  If no read arguments are given then every
       read  in  the  database or database block is displayed.  Otherwise the input file or the list of supplied
       integer ranges give the ordinal positions in the actively loaded portion of the db.  In  the  case  of  a
       file,  it  should simply contain a read index, one per line.  In the other case, a read range is either a
       lone integer or the symbol $, in which case the read range consists of just that read (the last  read  in
       the  database  if $).  One may also give two positive integers separated by a dash to indicate a range of
       integers, where again a $ represents the index of the last read in the actively loaded db.  For  example,
       1  3-5 $ displays reads 1, 3, 4, 5, and the last read in the active db.  As another example, 1-$ displays
       every read in the active db (the default).

       By default a .fasta file of the read sequences is displayed.  If the  -q  option  is  set,  then  the  QV
       streams  are  also displayed in a non-standard modification of the fasta format.  If the -n option is set
       then the DNA sequence is not displayed.  If the -Q option is set then a .quiva file is displayed  and  in
       this case the -n and -m options may not be set (and the -q and -w options have no effect).

       If  one  or  more  masks  are  set  with  the -m option then the track intervals are also displayed in an
       additional header line and the bases within an interval are displayed in the case opposite that used  for
       all  the  other  bases.  By default the output sequences are in lower case and 80 chars per line.  The -U
       option specifies upper case should be used, and the characters per line, or line width, can be set to any
       positive value with the -w option.

       The  .fasta or .quiva files that are output can be converted into a DB by fasta2DB(1) and quiva2DB(1) (if
       the -q and -n options are not set and no -m options are set), giving one a simple way to make a DB  of  a
       subset of the reads for testing purposes.

SEE ALSO

       daligner(1)