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NAME

       Maqview - Maq alignment indexer and viewer

SYNOPSIS

       maqindex -i|-v|-b [-c in.cns] in.map [chr[:start[-end]] [...]]

       maqview [-c in.cns] in.map

DESCRIPTION

       Maqview is a set of programs that achieves fast random access to the
       alignment file generated by `maq map', and displays the alignment with
       a nice GUI (Graphical User Interface). It is highly efficient in speed,
       memory and disk usage. Maqview is based on OpenGL and is known to work
       on both Mac OS X and Linux. Porting to Windows is in principle easy.

   maqindex
       maqindex -i|-v|-b [-c in.cns] in.map [chr[:start[-end]] [...]]

       -i       Index the alignment file

       -v       Print the alignment in the specified region in the `maq
                mapview' format

       -b       Dump the alignment in the specified region in the binary .map
                format

       -c FILE  Index the Maq consensus file for viewing in maqview at the
                same time

       Program maqindex indexes a maq alignment file in.map or quickly
       retrieves all the reads in one or multiple regions. One of -i, -v and
       -b must be used. For -v or -b, at least one region like `chrX',
       `chrX:1000' or `chrX:1,000-2,000' must be specified. Multiple regions
       are allowed.

   maqview
       maqview [-c in.cns] in.map

       -c FILE  The Maq consensus file

       Program maqview displays the read alignment in a graphical window. When
       in.cns is specified, the top sequence is the reference, followed by the
       Maq consensus sequence; otherwise, the majority-rule consensus will be
       calculated.

       Maqview has two views: sequence view and box view. In the sequence
       view, read sequences will be printed on the screen. Darker bases
       indicate lower base qualities and red ones show the differences in
       comparison to the reference if in.cns is speficied or to the majority-
       rule consensus if not. In the box view, different types of nucleotides
       are represented as colour boxes with green for A, cyan for C, orange
       for G, red for T and dark gray for N. The saturation of colours
       indicates the base qualities and the thickness lines of reads shows the
       mapping qualities of read alignments. Zooming in/out is supported only
       in the box view. In both views, the status bar at the bottom of the
       window will show some information about the key touches, and read names
       and base qualities pointed by the mouse.

       Navigating the alignment is accomplished by vaious key bindings.

       · Key bindings:

          ?                Display help
          <Esc>            Exit
          <F1>             Sequence view
          <F2>             Box view
          p                Switch to the previous reference sequence
          n                Switch to the next reference sequence
          r                Refresh

          <digits> <Enter> Move to the position pointed by <digits>
          h / <Left>       Move left by one base
          l / <Right>      Move right by one base
          k / <Up>         Move up by one line
          j / <Down>       Move down by one line
          >                Move to the next read
          <                Move to the previous read
          g / <Home>       Move to the begining of the current reference
          G / <End>        Move to the end of the current reference
          u / <PageUp>     Move left by one page
          <Space>/<PageDn> Move right by one page
          <Shift> <Arrow>  Move by 100 bases
          <Ctrl> <Arrow>   Move by 1000 bases

          <Ctrl> +         Add a new view
          <Ctrl> -         Remove the current view

          <Enter>          Toggle on/off right auto-scrolling
          ^b               Toggle on/off left auto-scrolling
          +                Zoom in
          -                Zoom out
          0                Zoom to the default scale
          q                Toggle show/hide mapping qualities
          e                Toggle display SE/PE mapping qualities
          o                Open a new alignment file

       · Enter an integer and then press <Enter> to jump to the required
         position.

       · Enter an integer and then press a key other than <Enter> to speed up
         scrolling by the specified factor.

       · Left click and drag the yellow cross in the square to move along the
         sequence. Right click the reference to highlight a column.

LICENSE

       GNU General Public License (GPL)

AVAILABILITY

       <http://maq.sourceforge.net>

AUTHORS

       Jue Ruan <ruanjue@genomics.org.cn> for writing and maintaining the
       whole software.

       Heng Li <lh3@sanger.ac.uk> for testing the program and drafting the
       documentations.

       Mengyao Zhao <zhaomengyao@gmail.com> for designing the color schemes.



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