Use new script for checking Illumina data files

[Nicklas Nordborg]

The picard program (see #631) mostly checks that data files exists and have a reasonable size. We have developed another script that also performs some basic checking of the correctness of the data files: /usr/local/packages/genseq_tools/v0.01/genseq_check_illumina_dir.pl

-t parameter is used to specify lane: -t 1, -t 1,2,5 (it can also be used to specify tiles but we are not interested in this)

-c parameter can be used to specify cycles to check. We can use this to skip checking cycles which are excluded by the read string.

Output is simple. If all checked are ok:

Format: bcl.bgzf - complete

If there are any problems:

Format: bcl+clocs - with errors
Missing: L001/C101.1/s_1_1101.bcl
Missing: L001/C102.1/s_1_1101.bcl
Missing: L001/C103.1/s_1_1101.bcl
Missing: L001/C104.1/s_1_1101.bcl 

[Nicklas Nordborg]

(In [2910]) Fixes #689: Use new script for checking Illumina data files

It is now possible to select if Picard or the genseq script should be used for checking. It is also possible to select which lanes that should be checked.

The path to the genseq script must be specified in reggie-config.xml.

[Nicklas Nordborg]

(In [2920]) References #689: Use new script for checking Illumina data files

Preserve line breaks.