Handle paired-end eland files.
authorDiane Trout <diane@caltech.edu>
Wed, 24 Dec 2008 23:39:31 +0000 (23:39 +0000)
committerDiane Trout <diane@caltech.edu>
Wed, 24 Dec 2008 23:39:31 +0000 (23:39 +0000)
commit121e3f07342d1a9889dff2d0f2bacf16e65f0d66
treef88146a8198b362fa904c205e57328d6d501207d
parent748b1ed537300bff37b17bf741d0300839d6d743
Handle paired-end eland files.

This required changing the ELAND class to hold a list of dictionaries
from its previous implmentation where it was exporting an internal dictionary
of the lanes.

I decided to directly show the internal list and to remove the previous
dictionary methods to make it more obvious when code was expecting
the previous behavior.

Also a saved runfolder will now have eland files of the form
s_<lane id>_<end id>.

Internally the end is 0 or 1, I tried to make the display show 1 or 2 for
the users benefit though.
htsworkflow/pipelines/eland.py
htsworkflow/pipelines/runfolder.py
htsworkflow/pipelines/test/simulate_runfolder.py
htsworkflow/pipelines/test/test_runfolder026.py
htsworkflow/pipelines/test/test_runfolder030.py
htsworkflow/pipelines/test/test_runfolder110.py
htsworkflow/pipelines/test/test_runfolder_ipar100.py
htsworkflow/pipelines/test/test_runfolder_pair.py