12/08/2010
COMMITS:
    08b896832ed8ca4ef78682c8a80f6f6955baee9d,
    9600985f364b4834c26b46fa8a849b531c68b558,
    75414a50f48a1ad9fefebfcd33ebefd7a8bc2d07

Modifications for the sequence translation update (diffs are highlighted within the files):
    lib/bam/BamInterface.cpp
    lib/bam/BamInterface.h
    lib/bam/GenericSamInterface.h
    lib/bam/SamFile.cpp
    lib/bam/SamFile.h
    lib/bam/SamInterface.cpp
    lib/bam/SamInterface.h
    lib/bam/SamQuerySeqWithRefHelper.cpp
    lib/bam/SamQuerySeqWithRefHelper.h
    lib/bam/SamRecord.cpp
    lib/bam/SamRecord.h

 TestFiles
  Modified Test Files:
    lib/bam/test/Main.cpp
    lib/bam/test/Makefile.testtool
  New Test Files:
    lib/bam/test/TestEquals.cpp
    lib/bam/test/TestEquals.h
    lib/bam/test/expected/testEqWithBases.bam
    lib/bam/test/expected/testEqWithBases.sam
    lib/bam/test/expected/testEqWithEq.bam
    lib/bam/test/expected/testEqWithEq.sam
    lib/bam/test/expected/testEqWithOrig.bam
    lib/bam/test/expected/testEqWithOrig.sam
    lib/bam/test/test.sh
    lib/bam/test/testFiles/testEq.bam
    lib/bam/test/testFiles/testEq.sam
  The following files were moved to a new directory and replaced with a link:
    src/bam/test/testFiles/chr1_partial-bs.umfa
    src/bam/test/testFiles/chr1_partial-bs.umfa
    src/bam/test/testFiles/chr1_partial.fa
    src/bam/test/testFiles/chr1_partial.fa
  Moved to:
    lib/bam/test/testFiles/chr1_partial-bs.umfa
    lib/bam/test/testFiles/chr1_partial.fa