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)