Commit [r83] Maximize Restore History

Fixed some bugs and added functionality to Honey

acenglishbcm 2014-03-20

added /trunk/pbsuite/honey/Force.py
changed /trunk/docs/HoneyReadme.txt
changed /trunk/docs/jellyExample/data/reads/filtered_subreads.fastq
changed /trunk/pbsuite/banana/OLCAssembly.py
changed /trunk/pbsuite/honey/HSpots.py
changed /trunk/pbsuite/honey/Honey.py
changed /trunk/pbsuite/honey/TGraf.py
changed /trunk/pbsuite/honey/__init__.py
changed /trunk/pbsuite/honey/bampie.py
changed /trunk/pbsuite/jelly/m4pie.py
changed /trunk/pbsuite/utils/CommandRunner.py
/trunk/pbsuite/honey/Force.py Diff Switch to side-by-side view
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/trunk/docs/HoneyReadme.txt Diff Switch to side-by-side view
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/trunk/docs/jellyExample/data/reads/filtered_subreads.fastq Diff Switch to side-by-side view
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/trunk/pbsuite/banana/OLCAssembly.py Diff Switch to side-by-side view
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/trunk/pbsuite/honey/HSpots.py Diff Switch to side-by-side view
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/trunk/pbsuite/honey/Honey.py Diff Switch to side-by-side view
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/trunk/pbsuite/honey/TGraf.py Diff Switch to side-by-side view
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/trunk/pbsuite/honey/__init__.py Diff Switch to side-by-side view
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/trunk/pbsuite/honey/bampie.py Diff Switch to side-by-side view
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/trunk/pbsuite/jelly/m4pie.py Diff Switch to side-by-side view
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/trunk/pbsuite/utils/CommandRunner.py Diff Switch to side-by-side view
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