DBshow(1) display reads stored in a Dazzler database


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


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.