Initial import of //depot/software/bioinformatics/tools/kineticsTools/ from the state at revision @127694

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 127694]
Merging using mainline-to-S2.1

bug 20574

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 127713]
remove use of ReferenceEntry -- ipdSummary.py must be passed the full reference path
bug 24117

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 128233]
Bug 24117. Update reference path in tests.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 128335]
Bug 24117.
       Initial stab at refactoring to support multi-site detection.
       Pull out mixture estimation methods into a common class;  previously there were copies of methods in KineticWorker and ModificationDecode.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 128739]
use smaller chunks in smaller inter-process queues in ipdSummary.py
appears to keep the memory consumption under better control
bug 24059

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 129002]
speed / scalability fixes developed on Arabadopsis. 80x arabadopsis now takes ~5hr and completes reliably.
update the test data to p4-c2.
bug 241174

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 129611]
bug 24117

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 129622]
include my crack at MultiSiteDetection -- not ready for primetime yet.
bug 24117

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 129652]
bug 23997 - ran autopep8 to get the kineticsTools jenkins project to stable

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 129738]
fix issue I introduced in extra field handling
bug 24117

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 129779]
blurb on strand conventions
bug 24117

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 129868]
Back out changelist 129622

(I help Khai get her code on her personal github)

[bug 24117]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 129871]
Previous backout didn't work correctly

Remove remaining disused files

[Bug 24117]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 129872]