Update sam libraries to 1.89

IGV-1904 #close
Modify build.xml so we can run tests without compiling main source
Add searching of negative strand to MotifFinderSource

Both the positive and negative strand are searched. What this means is that the sequence a user enters will be searched for on the  loaded sequence, and it's reverse complement. The feature is displayed at the positive-strand coords in either case.

This is not very efficient at the moment, we reverse-complement each chunk of sequence rather than the user-entered motif. This also means the returned order is backwards, so we need to do some reversing and combining of collections to give features in the proper order. Since this developer doesn't know how to reverse-complement a regex, we went this way.

Refactored some test code as well

IGV-1905 #resolve
Set cufflinks_plugin to invisible
Adjust test target dependencies

So that our "tests" target still compiles source as necessary.
Wrap text by word in MotifFinderDialog
Ignore testSearchWholeChromo
Change test_nocompile -> tests_nocompile
Support for sorting and indexing mutation files (.mut and .maf).
Reinsert feature track loading "case" in TrackLoader, unintentionally removed.
Change order of fields in MotifFinderDialog
Add test for loading BAM from ftp
Performance improvement of MotifFinderSource

Don't clone sequence, just reverse-complement in place
Add test for loading BAM from ftp headed
Remove BLAT menu items
Remove radio buttons for choosing string type in MotifFinder

We just auto-detect the type and display an error if it's bad
Update headed testLoadBamFTP

So that it actually tests properly
Update IGVSessionReaderTestHeaded

Ignore test file for which data is missing, update one feature match session now that we match the negative strand
Add test for loading a bed file from FTP

Currently failing, this is a real bug

IGV-1910
Use updated tribble which properly handles registerHelperClass

Tribble built on this developers machine (Mac OSX 10.7.5, ant 1.8.4) using:
 ant -Dant.build.javac.target="1.6" -Dant.build.javac.source="1.6" -Dsam-version="r1414" clean tribble-jar

IGV-1910