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)

1.0                                              September 2015                                        DBSHOW(1)