Clip

NAME

clip -- an Experiment File sequence clipper

SYNOPSIS

clip [-w length_1] [-u unknown_1] [-W length_2] [-U unknown_2] [-v] [-s start_offset] [-m minimum_extent] file ...

DESCRIPTION

Clip is a simple program to decide how much of the 3' end of a sequence, stored as an Experiment File, should be clipped off and ignored during assembly. The decision is made by simply counting the numbers of unknown bases (eg - or N) found within windows slid left to right along the sequence.

The file arguments, of which there can be several, are processed one at a time. Each argument is assumed to be a valid Experiment File. The sequence is read from the Experiment File SQ identifier; clipping is performed; and a QL identifier is appended to the file.

The clip position is calculated by sliding a window of length length_1 along the sequence starting from base start_offset. We stop once we find greater than or equal to unknown_1 unknown bases. At this stage two choices are available; to place our clip at the start position of our first window or to proceed from our current position plus half of length_1 using a second window. In the latter case we perform a similar operation to the first window, except using the length_2 and unknown_2 parameters. We will then set the clip to be the start position of this second window.

To only use one window (the default parameters) set the length_2 parameter to be 0 using -W 0.

The default arguments are -w 100 -u 5 -W 0 -U 0 -s 20 -m 15.

OPTIONS

-w length

Set the length for the first window to length

-u unknown

Stop sliding the first window when we have greater than or equal to unknown bases within the current window.

-W length

Set the length for the second window to length. Setting this value to zero prevents the second window calculations from being performed.

-U unknown

Stop sliding the second window when we have greater than or equal to unknown bases within the current window.

-v

Enable verbose output. This outputs information on which files are currently being clipped.

-s offset

Force the first window to start the calculations from position offset in the sequence. This can be useful to avoid poor data at the ar 5' end of a sequence.

-m extent

If the clip algorithm returns a clip value of less than extent bases from our start position, then reject this figure and set QR to 1.

SEE ALSO

See section ExperimentFile(4).See section trace_clip.