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