CSC

Error codes

The following errors can occur.

1. "Failed to open file of file names to screen against". Fatal failure to open the file of file names to screen against.
2. "Failed to open single file to screen against". Fatal failure to open the file to screen against.
3. "Failed to open file of file names to screen". Fatal failure to open the file of file names to screen.
4. "Failed to open single file to screen". Fatal failure to open the file to screen.
5. "Failed to open file of passed file names". Fatal failure to open the file of file names for readings that do not match.
6. "Failed to open file of failed file names". Fatal failure to open the file of file names for readings that match.
7. "Error: could not open vector file". An individual sequence file could not be opened.
8. "Error: could not read vector file". An individual sequence file could not be read.
9. "Error: could not hash vector file". An individual sequence file could not be prepared for comparison.
10. "Error: could not open experiment file". The file does not exist or is unreadable.
11. "Error: no sequence in experiment file".
12. "Error: sequence too short". The reading is shorter than the minimum match length.
13. "Error: could not write to experiment file". The disk is full or the file is write protected.
14. "Error: hashing problem". An error occurred in the comparison algorithm. Please report to staden-package@mrc-lmb.cam.ac.uk

Inconsistencies in the selection of options, such as selecting -I and -i, should also cause the usage message (shown below) to appear, and the program to terminate.

Usage: screen_seq [options and paramters] 
Where options and parameters are:
    [-l minimum match (25)]           [-m Max vector length (100000)]
    [-i readings to screen fofn]      [-I reading to screen]
    [-s seqs to screen against fofn]  [-S seq to screen against]
    [-t test only]
    [-p passed fofn]                  [-f failed fofn]